Import files (FASTA) from your staging area into your Narrative as an Assembly data object. - Please see the Data Upload/Download Guide for more information.
+ Please see the Data Upload/Download Guide for more information. technical-description : none diff --git a/ui/narrative/methods/batch_import_genome_from_staging/display.yaml b/ui/narrative/methods/batch_import_genome_from_staging/display.yaml index ceb82b2..4d8fbe5 100644 --- a/ui/narrative/methods/batch_import_genome_from_staging/display.yaml +++ b/ui/narrative/methods/batch_import_genome_from_staging/display.yaml @@ -77,6 +77,6 @@ parameters : description : |Import files (GenBank or GFF + FASTA) from your staging area into your Narrative as a Genome data object. - Please see the Data Upload/Download Guide for more information.
+ Please see the Data Upload/Download Guide for more information. technical-description : none diff --git a/ui/narrative/methods/import_attribute_mapping_from_staging/display.yaml b/ui/narrative/methods/import_attribute_mapping_from_staging/display.yaml index ec52234..ef32d6a 100644 --- a/ui/narrative/methods/import_attribute_mapping_from_staging/display.yaml +++ b/ui/narrative/methods/import_attribute_mapping_from_staging/display.yaml @@ -36,7 +36,7 @@ parameters : description : |Import a TSV or Excel file from your staging area into your Narrative as an Attribute Mapping data object. - Please see the Data Upload/Download Guide for more information.
+ Please see the Data Upload/Download Guide for more information. publications : - diff --git a/ui/narrative/methods/import_eschermap_from_staging/display.yaml b/ui/narrative/methods/import_eschermap_from_staging/display.yaml index 7203a1c..c1e7ce6 100644 --- a/ui/narrative/methods/import_eschermap_from_staging/display.yaml +++ b/ui/narrative/methods/import_eschermap_from_staging/display.yaml @@ -36,4 +36,4 @@ parameters : description : |Import a JSON file from your staging area into your Narrative as an KBaseFBA.EscherMap data object. - Please see the Data Upload/Download Guide for more information.
+ Please see the Data Upload/Download Guide for more information. diff --git a/ui/narrative/methods/import_fasta_as_assembly_from_staging/display.yaml b/ui/narrative/methods/import_fasta_as_assembly_from_staging/display.yaml index 1321620..d79fbef 100644 --- a/ui/narrative/methods/import_fasta_as_assembly_from_staging/display.yaml +++ b/ui/narrative/methods/import_fasta_as_assembly_from_staging/display.yaml @@ -49,4 +49,4 @@ parameters : description : |Import a FASTA file from your staging area into your Narrative as an Assembly data object. - Please see the Data Upload/Download Guide for more information.
+ Please see the Data Upload/Download Guide for more information. diff --git a/ui/narrative/methods/import_fasta_as_seqset_from_staging/display.yaml b/ui/narrative/methods/import_fasta_as_seqset_from_staging/display.yaml index 2cc8e2a..565ec96 100644 --- a/ui/narrative/methods/import_fasta_as_seqset_from_staging/display.yaml +++ b/ui/narrative/methods/import_fasta_as_seqset_from_staging/display.yaml @@ -65,4 +65,4 @@ parameters : description : |Import a FASTA file from your staging area into your Narrative as a Protein/DNA Sequence Set data object. - Please see the Data Upload/Download Guide for more information.
+ Please see the Data Upload/Download Guide for more information. diff --git a/ui/narrative/methods/import_fastq_interleaved_as_reads_from_staging/display.yaml b/ui/narrative/methods/import_fastq_interleaved_as_reads_from_staging/display.yaml index ef19b15..430b748 100644 --- a/ui/narrative/methods/import_fastq_interleaved_as_reads_from_staging/display.yaml +++ b/ui/narrative/methods/import_fastq_interleaved_as_reads_from_staging/display.yaml @@ -65,6 +65,6 @@ parameters : description : |Import a Interleaved FASTQ file from your staging area into your Narrative as an Assembly data object. - Please see the Data Upload/Download Guide for more information.
+ Please see the Data Upload/Download Guide for more information. technical-description : none diff --git a/ui/narrative/methods/import_fastq_noninterleaved_as_reads_from_staging/display.yaml b/ui/narrative/methods/import_fastq_noninterleaved_as_reads_from_staging/display.yaml index 802e54b..4bd1386 100644 --- a/ui/narrative/methods/import_fastq_noninterleaved_as_reads_from_staging/display.yaml +++ b/ui/narrative/methods/import_fastq_noninterleaved_as_reads_from_staging/display.yaml @@ -65,6 +65,6 @@ parameters : description : |Import a NonInterleaved FASTQ file into your Narrative as a Reads data object - Please see the Data Upload/Download Guide for more information.
+ Please see the Data Upload/Download Guide for more information. technical-description : none diff --git a/ui/narrative/methods/import_fastq_sra_as_reads_from_staging/display.yaml b/ui/narrative/methods/import_fastq_sra_as_reads_from_staging/display.yaml index fcdefa7..775b0ad 100644 --- a/ui/narrative/methods/import_fastq_sra_as_reads_from_staging/display.yaml +++ b/ui/narrative/methods/import_fastq_sra_as_reads_from_staging/display.yaml @@ -79,6 +79,6 @@ parameters : description : |Import a FASTQ/SRA file into your Narrative as a Reads data object - Please see the Data Upload/Download Guide for more information.
+ Please see the Data Upload/Download Guide for more information. technical-description : none diff --git a/ui/narrative/methods/import_file_as_fba_model_from_staging/display.yaml b/ui/narrative/methods/import_file_as_fba_model_from_staging/display.yaml index c426812..6576c07 100755 --- a/ui/narrative/methods/import_file_as_fba_model_from_staging/display.yaml +++ b/ui/narrative/methods/import_file_as_fba_model_from_staging/display.yaml @@ -64,4 +64,4 @@ parameters : description : |Import a file in TSV, XLS (Excel) or SBML format from your staging area into your Narrative as an FBAModel. - Please see the Data Upload/Download Guide for more information.
+ Please see the Data Upload/Download Guide for more information. diff --git a/ui/narrative/methods/import_genbank_as_genome_from_staging/display.yaml b/ui/narrative/methods/import_genbank_as_genome_from_staging/display.yaml index 5d4f6ee..c4c5453 100644 --- a/ui/narrative/methods/import_genbank_as_genome_from_staging/display.yaml +++ b/ui/narrative/methods/import_genbank_as_genome_from_staging/display.yaml @@ -93,4 +93,4 @@ parameters : description : |Import a GenBank file from your staging area into your Narrative as a Genome data object. - Please see the Data Upload/Download Guide for more information.
+ Please see the Data Upload/Download Guide for more information. diff --git a/ui/narrative/methods/import_gff_fasta_as_genome_from_staging/display.yaml b/ui/narrative/methods/import_gff_fasta_as_genome_from_staging/display.yaml index a576892..03b6850 100644 --- a/ui/narrative/methods/import_gff_fasta_as_genome_from_staging/display.yaml +++ b/ui/narrative/methods/import_gff_fasta_as_genome_from_staging/display.yaml @@ -94,6 +94,6 @@ parameters : description : |Import a GFF or FASTA file from your staging area into your Narrative as a Genome data object. - Please see the Data Upload/Download Guide for more information.
+ Please see the Data Upload/Download Guide for more information. technical-description : none diff --git a/ui/narrative/methods/import_gff_fasta_as_metagenome_from_staging/display.yaml b/ui/narrative/methods/import_gff_fasta_as_metagenome_from_staging/display.yaml index b3f10a2..29c6899 100644 --- a/ui/narrative/methods/import_gff_fasta_as_metagenome_from_staging/display.yaml +++ b/ui/narrative/methods/import_gff_fasta_as_metagenome_from_staging/display.yaml @@ -74,6 +74,6 @@ parameters : description : |Import a GFF or FASTA file from your staging area into your Narrative as a Genome data object. - Please see the Data Upload/Download Guide for more information.
+ Please see the Data Upload/Download Guide for more information. technical-description : none diff --git a/ui/narrative/methods/import_sra_as_reads_from_staging/display.yaml b/ui/narrative/methods/import_sra_as_reads_from_staging/display.yaml index a1bc6c6..93c97c2 100644 --- a/ui/narrative/methods/import_sra_as_reads_from_staging/display.yaml +++ b/ui/narrative/methods/import_sra_as_reads_from_staging/display.yaml @@ -58,6 +58,6 @@ parameters : description : |Import a SRA file from your staging area into your Narrative as READS data object. - Please see the Data Upload/Download Guide for more information.
+ Please see the Data Upload/Download Guide for more information. technical-description : none diff --git a/ui/narrative/methods/import_sra_as_reads_from_web/display.yaml b/ui/narrative/methods/import_sra_as_reads_from_web/display.yaml index 4a45187..a78a5ba 100644 --- a/ui/narrative/methods/import_sra_as_reads_from_web/display.yaml +++ b/ui/narrative/methods/import_sra_as_reads_from_web/display.yaml @@ -58,13 +58,13 @@ parameter-groups : short-hint : SRA file URL and output Reads file name. description : | -This App allows the user to load SRA format read libraries directly into the workspace from sources on the web. In addition to standard HTTP and anonymous FTP links, the user may also obtain files from Google drive and Dropbox links. Please see the FASTQ/SRA Reads Data Upload/Download Guide for more information about SRA reads libraries.
+This App allows the user to load SRA format read libraries directly into the workspace from sources on the web. In addition to standard HTTP and anonymous FTP links, the user may also obtain files from Google drive and Dropbox links. Please see the FASTQ/SRA Reads Data Upload/Download Guide for more information about SRA reads libraries.
Using the app
The user must inform KBase about the nature of the URL link by selecting one of the choices in the “URL Type” pulldown menu. “Direct” means the link is a standard WWW URL, “FTP link” means anonymous FTP, and “Dropbox” and “Google Drive” Public Shared Links are for shared files in those two sources (see below for more instructions in those two cases).
Once the link type is selected, the user can enter one or more URL links of that type. For each link, hit the “+” button to open a new sub-panel for the link. In each sub-panel, mandatory or required entries are indicated by a red vertical bar on the right. The first entry field takes the actual web link URL (by typing or pasting). The second is the object name you want to give to the reads object once it is loaded into KBase. The third mandatory field is a checkbox indicating whether or not the reads belong to a single genome. The remaining optional information are metadata describing the reads. More detail can be found under the hints for each field.
-If your reads are in a publicly accessible URL, you can directly import the reads into your Narrative using either this App, the Import Paired-End Reads from Web App, or the Import Single-End Reads from Web Apps.
+If your reads are in a publicly accessible URL, you can directly import the reads into your Narrative using either this App, the Import Paired-End Reads from Web App, or the Import Single-End Reads from Web Apps.
How to Use a ‘Google Drive Public Shared Link’
In the source location in Google Drive:
Import TSV File as Expression Matrix From Staging Area
This uploader enables you to upload a gene expression data matrix in TSV (Tab-Separated Values) format.
The .tsv file is a tab-delimited text file, with genes down the rows and sample/observations across the columns (see http://kbase.us/data-upload-download-guide/expression-matrix/ for more information). Make sure the first label in the first column +
The .tsv file is a tab-delimited text file, with genes down the rows and sample/observations across the columns (see https://docs.kbase.us/data/upload-download-guide/expression-matrix for more information). Make sure the first label in the first column is "gene-id" followed by tab-delimited labels for samples. Each row (gene) should have an identifier (in green) that always goes in the first column. Each column (sample) should have a label (in blue) that is always in the first row. The remaining cells in the table contain expression values for the appropriate gene and sample. Be sure to exclude gene features for which all expressions are missing or are the same for all the conditions/samples. See the - Data Upload and Download Guide for more information about formatting your expression data file.
+ Data Upload and Download Guide for more information about formatting your expression data file. diff --git a/ui/narrative/methods/import_tsv_excel_as_media_from_staging/display.yaml b/ui/narrative/methods/import_tsv_excel_as_media_from_staging/display.yaml index 178b8cc..4832c16 100644 --- a/ui/narrative/methods/import_tsv_excel_as_media_from_staging/display.yaml +++ b/ui/narrative/methods/import_tsv_excel_as_media_from_staging/display.yaml @@ -34,4 +34,4 @@ parameters : description : |Import Media file (TSV/Excel) from Staging Area - Please see the Data Upload/Download Guide for more information.
+ Please see the Data Upload/Download Guide for more information. diff --git a/ui/narrative/methods/load_paired_end_reads_from_URL/display.yaml b/ui/narrative/methods/load_paired_end_reads_from_URL/display.yaml index 1285c6b..b914819 100644 --- a/ui/narrative/methods/load_paired_end_reads_from_URL/display.yaml +++ b/ui/narrative/methods/load_paired_end_reads_from_URL/display.yaml @@ -63,9 +63,9 @@ parameter-groups : short-hint : FASTQ file URL and output reads filename. description : | -This App allows users to load FASTQ format paired-end read libraries directly into the workspace from sources on the web. In addition to standard HTTP and anonymous FTP links, the user may also obtain files from Google drive and Dropbox links. Please see the FASTQ/SRA Reads Data Upload/Download Guide for more information.
+This App allows users to load FASTQ format paired-end read libraries directly into the workspace from sources on the web. In addition to standard HTTP and anonymous FTP links, the user may also obtain files from Google drive and Dropbox links. Please see the FASTQ/SRA Reads Data Upload/Download Guide for more information.
-If your reads are in a publicly accessible URL, you can directly import the reads into your Narrative using either this App, the Import Single-End Reads from Web App, or Import SRA File as Reads from Webthe App.
+If your reads are in a publicly accessible URL, you can directly import the reads into your Narrative using either this App, the Import Single-End Reads from Web App, or Import SRA File as Reads from Webthe App.
How to Use a ‘Google Drive Public Shared Link’
In the source location in Google Drive:
Import Paired-End Reads from Staging Area - Please see the Data Upload/Download Guide for more information.
+ Please see the Data Upload/Download Guide for more information. technical-description : none diff --git a/ui/narrative/methods/load_single_end_reads_from_URL/display.yaml b/ui/narrative/methods/load_single_end_reads_from_URL/display.yaml index baf2882..c946d90 100644 --- a/ui/narrative/methods/load_single_end_reads_from_URL/display.yaml +++ b/ui/narrative/methods/load_single_end_reads_from_URL/display.yaml @@ -46,9 +46,9 @@ parameter-groups : short-hint : FASTQ file URL and output Reads file name. description : | -This App allows users to load FASTQ format single-end read libraries directly into the workspace from sources on the web. In addition to standard HTTP and anonymous FTP links, the user may also obtain files from Google drive and Dropbox links. Please see the FASTQ/SRA Reads Data Upload/Download Guide for more information.
+This App allows users to load FASTQ format single-end read libraries directly into the workspace from sources on the web. In addition to standard HTTP and anonymous FTP links, the user may also obtain files from Google drive and Dropbox links. Please see the FASTQ/SRA Reads Data Upload/Download Guide for more information.
-If your reads are in a publicly accessible URL, you can directly import the reads into your Narrative using either this App, the Import Paired-End Reads from Web App, or the Import SRA File as Reads from WebApp.
+If your reads are in a publicly accessible URL, you can directly import the reads into your Narrative using either this App, the Import Paired-End Reads from Web App, or the Import SRA File as Reads from WebApp.
How to Use a ‘Google Drive Public Shared Link’
In the source location in Google Drive: