Mercurial > repos > guerler > springsuite
comparison spring_minz.xml @ 2:cc21dac19d25 draft
"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1-dirty"
| author | guerler |
|---|---|
| date | Fri, 31 Jul 2020 01:49:36 -0400 |
| parents | d30785e31577 |
| children | c4b2e16845ab |
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| 1:56ad4e20f292 | 2:cc21dac19d25 |
|---|---|
| 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 $inputs |
| 7 link '${str(input)}' 'inputs/${input.name}' && | 7 #try |
| 8 echo '${input.name}' >> 'input_list' && | 8 ln -s '${str(input)}' 'inputs/${input.name}' && |
| 9 #end for && | 9 echo '${input.name}' >> 'input_list' && |
| 10 #except | |
| 11 #pass | |
| 12 #end try | |
| 13 #end for | |
| 10 python3 '$__tool_directory__/spring_minz.py' -m '$minscore' -t '$target' -c '$crossreference' -o '$output' -l input_list -i inputs | 14 python3 '$__tool_directory__/spring_minz.py' -m '$minscore' -t '$target' -c '$crossreference' -o '$output' -l input_list -i inputs |
| 11 ]]></command> | 15 ]]></command> |
| 12 <inputs> | 16 <inputs> |
| 13 <param format="data" name="target" type="data" label="Target Sequence" help="Homology search results of query sequence `hhr`. (-t)"/> | 17 <param format="data" name="target" type="data" label="Target Sequence" help="Homology search results of query sequence `hhr`. (-t)"/> |
| 14 <param format="data" name="inputs" type="data_collection" collection_type="list" label="Input Sequences" help="Homology search results of target sequences `hhr`. (-i)"/> | 18 <param format="data" name="inputs" type="data_collection" collection_type="list" label="Input Sequences" help="Homology search results of target sequences `hhr`. (-i)"/> |