Mercurial > repos > iuc > meme_fimo

comparison fimo.xml @ 7:de3c73f58451 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit ef11594cf3ca79e444ab4e30d83de5951a636faf
author iuc
date Sun, 10 Jul 2016 09:01:50 -0400
parents 3357222bd843
children b69b8c6bbbde
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6:3357222bd843 7:de3c73f58451
1 <tool id="meme_fimo" name="FIMO" version="4.11.0.4"> 1 <tool id="meme_fimo" name="FIMO" version="4.11.1.0">
2 <description>- Scan a set of sequences for motifs.</description> 2 <description>- Scan a set of sequences for motifs.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="6.9.3">imagemagick</requirement> 4 <requirement type="package" version="1.3.20">graphicsmagick</requirement>
5 <requirement type="package" version="4.11.0">meme</requirement> 5 <requirement type="package" version="4.11.1">meme</requirement>
6 </requirements> 6 </requirements>
7 <stdio>
8 <!-- Anything other than zero is an error -->
9 <exit_code range="1:" />
10 <!-- In case the return code has not been set propery check stderr too -->
11 <regex match="Error:" />
12 <regex match="Exception:" />
13 </stdio>
7 <command> 14 <command>
8 <![CDATA[ 15 <![CDATA[
9 mkdir -p output && 16 mkdir -p output &&
10 python $__tool_directory__/fimo_wrapper.py 17 python $__tool_directory__/fimo_wrapper.py
11 --input_motifs "${input_motifs}" 18 --input_motifs "${input_motifs}"
253 <test> 260 <test>
254 <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/> 261 <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/>
255 <param name="fasta_type_selector" value="history"/> 262 <param name="fasta_type_selector" value="history"/>
256 <param name="input_database" value="phiX.fasta" ftype="fasta"/> 263 <param name="input_database" value="phiX.fasta" ftype="fasta"/>
257 <param name="options_type_selector" value="advanced"/> 264 <param name="options_type_selector" value="advanced"/>
258 <param name="parse_genomic_coord" value="--parse_genomic_coord"/> 265 <param name="parse_genomic_coord" value="yes"/>
259 <param name="remove_duplicate_coords" value="yes"/> 266 <param name="remove_duplicate_coords" value="yes"/>
260 <param name="output_separate_motifs" value="yes"/> 267 <param name="output_separate_motifs" value="yes"/>
261 <param name="non_commercial_use" value="True"/> 268 <param name="non_commercial_use" value="True"/>
262 <output name="html_outfile" file="fimo_output_html_2.html" compare="contains"/> 269 <output name="html_outfile" file="fimo_output_html_2.html" compare="contains"/>
263 <output name="txt_outfile" file="fimo_output_txt_2.txt" compare="contains"/> 270 <output name="txt_outfile" file="fimo_output_txt_2.txt" compare="contains"/>