Mercurial > repos > iuc > meme_fimo
comparison fimo.xml @ 8:53846f74a019 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit ef11594cf3ca79e444ab4e30d83de5951a636faf
| author | iuc |
|---|---|
| date | Sun, 10 Jul 2016 09:02:14 -0400 |
| parents | b3f7ff168b9a |
| children | 307b2f3559bf |
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| 7:b3f7ff168b9a | 8:53846f74a019 |
|---|---|
| 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"/> |