# HG changeset patch
# User ieguinoa
# Date 1540158528 14400
# Node ID bacd91d8b05a4336f28239f6d05eb2f1e2de1444
# Parent d71f65b854de32ee92c0d39b186de71ba0cdcf9a
Uploaded
diff -r d71f65b854de -r bacd91d8b05a data_manager/.Rhistory
diff -r d71f65b854de -r bacd91d8b05a data_manager/data_manager_fetch_tx2gene.xml
--- a/data_manager/data_manager_fetch_tx2gene.xml Fri Oct 19 07:36:02 2018 -0400
+++ b/data_manager/data_manager_fetch_tx2gene.xml Sun Oct 21 17:48:48 2018 -0400
@@ -1,7 +1,7 @@
<tool id="data_manager_fetch_tx2gene" name="Create entries in tx2gene data table" version="0.0.1" tool_type="manage_data">
<description>fetching</description>
<requirements>
- <requirement type="package" version="1.26.4">bioconductor-genomicfeatures</requirement>
+ <requirement type="package" version="1.32.3">bioconductor-genomicfeatures</requirement>
<requirement type="package">r-getopt</requirement>
</requirements>
@@ -18,7 +18,7 @@
<param type="text" name="sequence_name" value="" label="Name of sequence" />
<param type="text" name="sequence_id" value="" label="ID for sequence" />
- <param name="file_type" type="select" label="Select input type: GFF/GTF file(features will be extracted to create tx2gene table) or transcript to gene table file(tab separated)">
+ <param name="file_type" type="select" label="Select input type: GFF/GTF file(features will be extracted to create tx2gene table) or transcript to gene table file(tab separated)" help="When using GFF3/GTF files as input, transcript feaatures must contain a transcript_id attribute.">
<option value="gtf">GTF file</option>
<option value="gff3">GFF3 file</option>
<option value="tx2gene">tx2gene</option>
@@ -60,7 +60,7 @@
<help>
**What it does**
-Fetches a gff file from various sources (URL, Galaxy History, or a server directory) and populates the "all_gff" data table.
+Populate the tx2gene data table with transcript-genes mapping tables.
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