Mercurial > repos > mvdbeek > r_goseq_1_22_0

diff get_length_and_gc_content.xml @ 0:a6427f7893b0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
author mvdbeek
date Fri, 26 Feb 2016 06:57:47 -0500
parents
children 0e9424413ab0
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_length_and_gc_content.xml	Fri Feb 26 06:57:47 2016 -0500
@@ -0,0 +1,47 @@
+<tool id="length_and_gc_content" name="gene length and gc content from gtf file" version="0.1.0">
+    <description />
+    <requirements>
+        <requirement type="package" version="3.2.1">R</requirement>
+        <requirement type="package" version="1.22.0">goseq</requirement>
+    </requirements>
+    <command interpreter="Rscript">
+        get_length_and_gc_content.r --gtf "$gtf"
+        #if $fastaSource.genomeSource == "indexed":
+            --fasta "$fastaSource.fasta_pre_installed.fields.path"
+        #else:
+            --fasta "$fastaSource.fasta_history"
+        #end if
+        --output "$output"
+    </command>
+    <inputs>
+        <param help="The GTF must match the FASTA file" label="GTF file for length and GC calculation" name="gtf" type="data" />
+        <conditional name="fastaSource">
+            <param help="choose history if you don't see the correct genome fasta" label="Select a reference fasta from your history or use a built-in fasta?" name="genomeSource" type="select">
+                <option value="indexed">Use a built-in fasta</option>
+                <option value="history">Use fasta from history</option>
+            </param>
+        <when value="indexed">
+            <param help="Select the fasta file from a list of pre-installed genomes" label="Select a fasta sequence" name="fasta_pre_installed" type="select">
+              <options from_data_table="all_fasta"/>
+            </param>
+        </when>
+        <when value="history">
+            <param format="fasta" label="Select a fasta file, to serve as index reference" name="fasta_history" type="data" />
+        </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="tabular" label="length and gc content" name="output" />
+    </outputs>
+    <tests></tests>
+    <help>
+
+        **What it does**
+
+        Returns a tabular file with gene name, length and GC content, based on a supplied GTF and a FASTA file.
+
+
+        </help>
+    <citations>
+    </citations>
+</tool>