Mercurial > repos > p.lucas > extract_fasta_subsequence

changeset 1:f2f198a2db78 draft

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Uploaded
author p.lucas
date Wed, 26 Sep 2018 08:27:18 -0400
parents 746e286edff0
children 7eb623472582
files exseq_multi.xml
diffstat 1 files changed, 34 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/exseq_multi.xml	Wed Sep 26 08:27:18 2018 -0400
@@ -0,0 +1,34 @@
+<tool id="extract_align" name="Extract sub sequence of multifasta file." version="0.1.0">
+    <description>Filter segment from gb file and headers text file.</description>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command>
+        python3 exseq_multi.py -i $inputfile -s $startpos -e $endpos -o $output
+    </command>
+    <inputs>
+        <param type="data" name="inputfile" format="fasta" label="Select your multifasta file :" />
+        <param type="text" name="startpos" label="Start position to cut :" /> 
+        <param type="text" name="endpos" label="End position to stop the cut :" /> 
+    </inputs>
+    <outputs>
+        <data name="output1" format="fasta" />
+    </outputs>
+    <help>
+         usage: exseq_multi.py [-h] [-i INFILE] [-s START] [-e END] [-o OUTFILE]
+ 
+         Extract sequence of multifasta file from position start/end.
+
+         optional arguments:
+          -h, --help            show this help message and exit
+          -i INFILE, --input_file INFILE
+                        Multifasta file.
+          -s START, --start_position START
+                        Start position to extract.
+          -e END, --end_position END
+                        End position to extract.
+          -o OUTFILE, --output_file OUTFILE
+                        Output file.
+
+    </help>
+</tool>