Mercurial > repos > guerler > springsuite
comparison spring_minz.xml @ 3:c4b2e16845ab draft
"planemo upload commit 63ddea9328a66c7a7bc5071e71128dad66481550"
| author | guerler |
|---|---|
| date | Fri, 31 Jul 2020 03:35:49 -0400 |
| parents | cc21dac19d25 |
| children | bde9a1a44a36 |
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| 2:cc21dac19d25 | 3:c4b2e16845ab |
|---|---|
| 1 <tool id="spring_minz" name="SPRING min-Z" version="0.1.0" python_template_version="3.5"> | 1 <tool id="spring_minz" name="SPRING min-Z" version="0.1.0" python_template_version="3.5"> |
| 2 <description>filter operation</description> | 2 <description>Filter operation</description> |
| 3 <code file="spring_minz.py"/> | 3 <code file="spring_minz.py"/> |
| 4 <command detect_errors="exit_code"><![CDATA[ | 4 <command detect_errors="exit_code"><![CDATA[ |
| 5 mkdir -p inputs && | 5 mkdir -p inputs && |
| 6 #for input in $inputs | 6 #for input in $inputs |
| 7 #try | 7 link '${str(input)}' 'inputs/${input.name}' && |
| 8 ln -s '${str(input)}' 'inputs/${input.name}' && | 8 echo '${input.name}' >> 'input_list' && |
| 9 echo '${input.name}' >> 'input_list' && | |
| 10 #except | |
| 11 #pass | |
| 12 #end try | |
| 13 #end for | 9 #end for |
| 14 python3 '$__tool_directory__/spring_minz.py' -m '$minscore' -t '$target' -c '$crossreference' -o '$output' -l input_list -i inputs | 10 python3 '$__tool_directory__/spring_minz.py' -m '$minscore' -t '$target' -c '$crossreference' -o '$output' -l input_list -i inputs |
| 15 ]]></command> | 11 ]]></command> |
| 16 <inputs> | 12 <inputs> |
| 17 <param format="data" name="target" type="data" label="Target Sequence" help="Homology search results of query sequence `hhr`. (-t)"/> | 13 <param format="data" name="target" type="data" label="Target Sequence" help="Homology search results of query sequence `hhr`. (-t)"/> |