Mercurial > repos > iuc > chira_extract
diff chira_extract.xml @ 11:a618f28e1496 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 51f68a6d51d9e87f8e54021ce760b1506a3589b8"
author | iuc |
---|---|
date | Sun, 14 Jun 2020 17:37:05 -0400 |
parents | 7ec1d063fecd |
children | 97ca48f470ef |
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--- a/chira_extract.xml Sat Jun 06 08:12:25 2020 -0400 +++ b/chira_extract.xml Sun Jun 14 17:37:05 2020 -0400 @@ -32,9 +32,12 @@ #end if $hybridize $seed_interaction + -sbp '$seed_bp' + -smpu '$seed_min_pu' + -acc '$accessibility' + -accw '$acc_width' + -m '$intarna_mode' $summarize - -a '$accessibility' - -m '$intarna_mode' -p "\${GALAXY_SLOTS:-2}" -o ./ ]]></command> @@ -93,29 +96,39 @@ <param name="hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false" label="Hybridize chimeric loci?" help="Turning this option on increases the run time of the tool significantly."/> - <param name="seed_interaction" type="boolean" truevalue="" falsevalue="--noSeed" checked="false" - label="Enforce seed interaction?"/> - <param name="accessibility" type="boolean" truevalue="C" falsevalue="N" checked="false" - label="Compute accessibility profiles for interacting sequences?"/> <param name="intarna_mode" type="select"> <option value="H">Heuristic</option> <option value="M">Exact</option> <option value="S">Seed-only</option> </param> + <param name="seed_interaction" type="boolean" truevalue="" falsevalue="--noSeed" checked="true" + label="Enforce seed interaction?"/> + <param name="seed_bp" type="integer" value="5" min="2" max="20" + label="Number of inter-molecular base pairs within the seed region" + help="IntaRNA --seedBP parameter"/> + <param name="seed_min_pu" type="float" value="0" min="0" max="1" + label="Minimal unpaired probability (per sequence) a seed region may have" + help="IntaRNA --seedMinPu parameter"/> + <param name="accessibility" type="boolean" truevalue="C" falsevalue="N" checked="false" + label="Compute accessibility profiles for interacting sequences?"/> + <param name="acc_width" type="integer" value="150" min="0" max="99999" + label="Sliding window size for accessibility computation" + help="IntaRNA --accW parameter"/> + <param name="temperature" type="float" value="37" min="0" max="100" + label="IntaRNA temperature parameter in Celsius to setup the VRNA energy parameters"/> <param name="summarize" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Summarize interactions at loci level?"/> </inputs> <outputs> <data format="tabular" name="chimeras" from_work_dir="chimeras" label="ChiRA chimeric reads on ${on_string}"/> - <data format="tabular" name="singletons" from_work_dir="singletons" label="ChiRA singleton reads on ${on_string}"/> <data format="tabular" name="interactions" from_work_dir="interactions" label="ChiRA interaction summary on ${on_string}"> <filter>summarize == True</filter> </data> </outputs> <tests> - <test expect_num_outputs="3"> + <test expect_num_outputs="2"> <param name="loci" value="loci.counts"/> <param name="ref_type" value="split"/> <param name="ref_fasta1" value="ref1.fasta"/> @@ -124,7 +137,6 @@ <param name="hybridize" value="true" /> <param name="summarize" value="true" /> <output name="chimeras" file="chimeras"/> - <output name="singletons" file="singletons"/> <output name="interactions" file="interactions"/> </test> </tests>