Mercurial > repos > guerler > springsuite
diff spring_minz.xml @ 23:5469e19f1f96 draft
"planemo upload commit 37a4c6844fd7ab1071ddf90f51915ec1a13c26b3"
| author | guerler |
|---|---|
| date | Thu, 29 Oct 2020 13:04:47 +0000 |
| parents | acaff61a09b2 |
| children | 802daf2993b0 |
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--- a/spring_minz.xml Wed Oct 28 06:49:58 2020 +0000 +++ b/spring_minz.xml Thu Oct 29 13:04:47 2020 +0000 @@ -2,59 +2,60 @@ <description>filter operation</description> <code file="spring_minz.py"/> <command detect_errors="exit_code"><![CDATA[ - mkdir -p inputs && - #for input in $inputs - link '${str(input)}' 'inputs/${input.element_identifier}' && - echo '${input.element_identifier}' >> 'input_list' && - #end for - mkdir -p targets && + mkdir -p targets && #for target in $targets link '${str(target)}' 'targets/${target.element_identifier}' && echo '${target.element_identifier}' >> 'target_list' && #end for - python3 '$__tool_directory__/spring_minz.py' -il input_list -ip inputs -tl target_list -tp targets -m '$minscore' -c '$crossreference' -x '$idx' -o '$output' + #if str($input_type.input_type_selector) == "true": + mkdir -p inputs && + #for input in $input_type.inputs + link '${str(input)}' 'inputs/${input.element_identifier}' && + echo '${input.element_identifier}' >> 'input_list' && + #end for + python3 '$__tool_directory__/spring_minz.py' -tl target_list -tp targets -il input_list -ip inputs -m '$minscore' -c '$crossreference' -x '$idx' -o '$output' -l '$log' + #else + python3 '$__tool_directory__/spring_minz.py' -tl target_list -tp targets -m '$minscore' -c '$crossreference' -x '$idx' -o '$output' -l '$log' + #end if ]]></command> <inputs> - <param format="txt" name="targets" type="data_collection" label="Target Profiles" help="Homology search result of target/query profiles `hhr`."/> - <param format="txt" name="inputs" type="data_collection" collection_type="list" label="Input Profiles" help="Homology search results of input profiles `hhr`."/> + <param format="txt" name="targets" type="data_collection" collection_type="list" label="Target Profiles" help="Homology search result of target/query profiles `hhr`."/> + <conditional name="input_type"> + <param name="input_type_selector" type="boolean" label="Identify interactions across sets?" checked="true"/> + <when value="true"> + <param format="txt" name="inputs" type="data_collection" collection_type="list" label="Input Profiles" help="Homology search results of input profiles `hhr`."/> + </when> + </conditional> <param format="txt" name="crossreference" type="data" label="Cross Reference" help="Cross reference of interacting proteins `first_id metadata_id second_id`."/> <param name="minscore" type="integer" label="Score threshold" value="10" min="1" max="200" help="Matching interaction pairs with a score lower than this threshold will be excluded."/> <param name="idx" type="integer" label="Identifier length" value="6" min="1" max="20" help="Specify the length of the identifier e.g. `1ACB_A` has length 6."/> </inputs> <outputs> - <data format="tabular" name="output" /> + <data format="tabular" name="output" label="SPRING min-Z Table"/> + <data format="txt" name="log" label="SPRING min-Z Log" /> </outputs> <tests> <test> <param name="targets"> <collection type="list"> - <element name="6WEY_A.hhr" value="6WEY_A.hhr" /> + <element name="7BQY_A.hhr" value="7BQY_A.hhr" /> + <element name="6WLC_A.hhr" value="6WLC_A.hhr" /> <element name="6WJI_A.hhr" value="6WJI_A.hhr" /> - <element name="6WLC_A.hhr" value="6WLC_A.hhr" /> - <element name="7BQY_A.hhr" value="7BQY_A.hhr" /> + <element name="6WEY_A.hhr" value="6WEY_A.hhr" /> <element name="6W37_A.hhr" value="6W37_A.hhr" /> <element name="6W9C_A.hhr" value="6W9C_A.hhr" /> + <element name="6W4H_B.hhr" value="6W4H_B.hhr" /> <element name="6W4H_A.hhr" value="6W4H_A.hhr" /> - <element name="6W4H_B.hhr" value="6W4H_B.hhr" /> <element name="6W9Q_A.hhr" value="6W9Q_A.hhr" /> </collection> </param> + <conditional name="input_type"> + <param name="input_type_selector" type="boolean" checked="false"/> + </conditional> <param name="idx" value="10"/> - <param name="inputs"> - <collection type="list"> - <element name="6WEY_A.hhr" value="6WEY_A.hhr" /> - <element name="6WJI_A.hhr" value="6WJI_A.hhr" /> - <element name="6WLC_A.hhr" value="6WLC_A.hhr" /> - <element name="7BQY_A.hhr" value="7BQY_A.hhr" /> - <element name="6W37_A.hhr" value="6W37_A.hhr" /> - <element name="6W9C_A.hhr" value="6W9C_A.hhr" /> - <element name="6W4H_A.hhr" value="6W4H_A.hhr" /> - <element name="6W4H_B.hhr" value="6W4H_B.hhr" /> - <element name="6W9Q_A.hhr" value="6W9Q_A.hhr" /> - </collection> - </param> <param name="crossreference" value="dbCAN_random.txt"/> <output name="output" file="dbCAN_result.txt"/> + <output name="log" file="dbCAN_log.txt"/> </test> <test> <param name="targets"> @@ -62,16 +63,20 @@ <element name="NP_000282.1.hhr" value="NP_000282.1.hhr" /> </collection> </param> - <param name="inputs"> - <collection type="list"> - <element name="NP_000282.1.hhr" value="NP_000282.1.hhr" /> - <element name="NP_000290.2.hhr" value="NP_000290.2.hhr" /> - <element name="NP_000548.2.hhr" value="NP_000548.2.hhr" /> - <element name="NP_000836.2.hhr" value="NP_000836.2.hhr" /> - </collection> - </param> + <conditional name="input_type"> + <param name="input_type_selector" type="boolean" checked="true"/> + <param name="inputs"> + <collection type="list"> + <element name="NP_000282.1.hhr" value="NP_000282.1.hhr" /> + <element name="NP_000290.2.hhr" value="NP_000290.2.hhr" /> + <element name="NP_000548.2.hhr" value="NP_000548.2.hhr" /> + <element name="NP_000836.2.hhr" value="NP_000836.2.hhr" /> + </collection> + </param> + </conditional> <param name="crossreference" value="pdb70_random.txt"/> <output name="output" file="pdb70_result.txt"/> + <output name="log" file="pdb70_log.txt"/> </test> </tests> <help><![CDATA[