Mercurial > repos > guerler > springsuite
diff spring_minz.xml @ 27:e34da554d415 draft
"planemo upload commit f12d400ea7827bb7d6b2ef31eb7f38e555bd053f-dirty"
| author | guerler |
|---|---|
| date | Sat, 31 Oct 2020 22:46:10 +0000 |
| parents | 124f82fbd986 |
| children | 41353488926c |
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--- a/spring_minz.xml Sat Oct 31 22:21:11 2020 +0000 +++ b/spring_minz.xml Sat Oct 31 22:46:10 2020 +0000 @@ -13,9 +13,9 @@ 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' -o '$output' -l '$log' + python3 '$__tool_directory__/spring_minz.py' -tl target_list -tp targets -il input_list -ip inputs -m '$minscore' -idx '$idx' -c '$crossreference' -o '$output' -l '$log' #else - python3 '$__tool_directory__/spring_minz.py' -tl target_list -tp targets -m '$minscore' -c '$crossreference' -o '$output' -l '$log' + python3 '$__tool_directory__/spring_minz.py' -tl target_list -tp targets -m '$minscore' -idx '$idx' -c '$crossreference' -o '$output' -l '$log' #end if ]]></command> <inputs> @@ -28,6 +28,7 @@ </conditional> <param format="tabular" 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" label="SPRING min-Z Table"/> @@ -37,18 +38,24 @@ <test> <param name="targets"> <collection type="list"> - <element name="NP_000836.2.hhr" value="minz/NP_000836.2.hhr" /> - <element name="NP_000548.2.hhr" value="minz/NP_000548.2.hhr" /> - <element name="NP_000282.1.hhr" value="minz/NP_000282.1.hhr" /> - <element name="NP_000290.2.hhr" value="minz/NP_000290.2.hhr" /> + <element name="7BQY_A.hhr" value="minz/7BQY_A.hhr" /> + <element name="6WLC_A.hhr" value="minz/6WLC_A.hhr" /> + <element name="6WJI_A.hhr" value="minz/6WJI_A.hhr" /> + <element name="6WEY_A.hhr" value="minz/6WEY_A.hhr" /> + <element name="6W37_A.hhr" value="minz/6W37_A.hhr" /> + <element name="6W9C_A.hhr" value="minz/6W9C_A.hhr" /> + <element name="6W4H_B.hhr" value="minz/6W4H_B.hhr" /> + <element name="6W4H_A.hhr" value="minz/6W4H_A.hhr" /> + <element name="6W9Q_A.hhr" value="minz/6W9Q_A.hhr" /> </collection> </param> <conditional name="input_type"> <param name="input_type_selector" type="boolean" checked="false"/> </conditional> - <param name="crossreference" value="minz/pdb70_random.txt"/> - <output name="output" file="minz/pdb70_result_0.txt"/> - <output name="log" file="minz/pdb70_log_0.txt"/> + <param name="crossreference" value="minz/dbCAN_random.txt"/> + <param name="idx" type="integer" value="10"/> + <output name="output" file="minz/dbCAN_result.txt"/> + <output name="log" file="minz/dbCAN_log.txt"/> </test> <test> <param name="targets"> @@ -68,8 +75,8 @@ </param> </conditional> <param name="crossreference" value="minz/pdb70_random.txt"/> - <output name="output" file="minz/pdb70_result_1.txt"/> - <output name="log" file="minz/pdb70_log_1.txt"/> + <output name="output" file="minz/pdb70_result.txt"/> + <output name="log" file="minz/pdb70_log.txt"/> </test> </tests> <help><![CDATA[