Mercurial > repos > marpiech > norwich_tools_dock
diff apoc.xml @ 2:958fa7ba4715 draft
planemo upload commit 489ad526806f22eefcb73e8d8efe44d648e8185e-dirty
| author | marpiech |
|---|---|
| date | Wed, 14 Sep 2016 09:47:48 -0400 |
| parents | dc6fb5c5d4c8 |
| children | 8c2e85bb2ce9 |
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--- a/apoc.xml Mon Sep 12 06:00:34 2016 -0400 +++ b/apoc.xml Wed Sep 14 09:47:48 2016 -0400 @@ -23,21 +23,22 @@ -fa $fa -pvol $pvol -plen $plen - #if $sod=="true" + #if $alignment_option.sod=="true" -sod #end if - -v $v - -m $m - #if $L - -L $L + -v $alignment_option.v + + -m $scoring_option.m + #if $scoring_option.L + -L $scoring_option.L #end if - #if $a=="true" + #if $scoring_option.a=="true" -a #end if - #if $b=="true" + #if $scoring_option.b=="true" -b #end if - #if $c=="true" + #if $scoring_option.c=="true" -c #end if @@ -64,8 +65,8 @@ <inputs> <conditional name="templates_source"> <param name="template_source_select" type="select" label="Chose template source: pdb file or file with list of templates"> - <option value="pdbfile">pdb file</option> - <option value="list">file with list of templates</option> + <option value="pdbfile">pdb file</option> + <option value="list">file with list of templates</option> </param> <when value="pdbfile"> <param name="pdbfile1" type="data" format="pdb" label="First (template) structure for comparison" help="(pdbfile1)" /> @@ -74,7 +75,7 @@ <when value="list"> <param name="lt" type="data" format="data" label="List of templates to compare in a file" help="(-lt)" /> <repeat name="template" title="pdb file from list of templates"> - <param name="input" type="data" format="pdb" label="pdbfile" /> + <param name="input" type="data" format="pdb" label="pdbfile" help="load all pdb files in the same order as in the list of templates" /> </repeat> </when> </conditional> @@ -90,7 +91,7 @@ <when value="list"> <param name="lq" type="data" format="data" label="List of queries (targets) to compare in a file." help="(-lq)" /> <repeat name="query" title="pdb file from list of queries"> - <param name="input" type="data" format="pdb" label="pdbfile" /> + <param name="input" type="data" format="pdb" label="pdbfile" help="load all pdb files in the same order as in the list of queries" /> </repeat> </when> </conditional> @@ -100,35 +101,39 @@ </param> <param name="pvol" type="text" value="1000" label="Minimal pocket volume in grid points" help="(-pvol)" /> <param name="plen" type="text" value="10" label="Minimal number of pocket residues" help="(-plen)" /> - <param name="sod" type="select" label="Restrict to sequence-order-dependent alignment" help="(-sod)"> - <option value="false" selected="true">Do not use this option</option> - <option value="true">Use this option</option> - </param> - <param name="v" type="select" label="Restrict to sequence-order-dependent alignment" help="(-v)"> - <option value="0">none</option> - <option value="1">concise</option> - <option value="2" selected="true">detailed</option> - </param> - <param name="m" type="select" label="Similarity scoring metric" help="(-m)"> - <option value="mt">TM-score</option> - <option value="ps" selected="true">PS-score</option> - </param> - <param name="L" type="text" label="Normalize the score with a fixed length specified by num" optional="true" help="(-L)" /> - <param name="a" type="select" label="Normalize the score by the average size of two structures" help="(-a)"> - <option value="false" selected="true">Do not use this option</option> - <option value="true">Use this option</option> - </param> - <param name="b" type="select" label="Normalize the score by the minimum size of two structures" help="(-b)"> - <option value="false" selected="true">Do not use this option</option> - <option value="true">Use this option</option> - </param> - <param name="c" type="select" label="Normalize the score by the maximum size of two structures" help="(-c)"> - <option value="false" selected="true">Do not use this option</option> - <option value="true">Use this option</option> - </param> + <section name="alignment_option" title="Alignment option"> + <param name="sod" type="select" label="Restrict to sequence-order-dependent alignment" help="(-sod)"> + <option value="false" selected="true">Do not use this option</option> + <option value="true">Use this option</option> + </param> + <param name="v" type="select" label="Restrict to sequence-order-dependent alignment" help="(-v)"> + <option value="0">none</option> + <option value="1">concise</option> + <option value="2" selected="true">detailed</option> + </param> + </section> + <section name="scoring_option" title="Scoring option"> + <param name="m" type="select" label="Similarity scoring metric" help="(-m)"> + <option value="tm">TM-score</option> + <option value="ps" selected="true">PS-score</option> + </param> + <param name="L" type="text" label="Normalize the score with a fixed length specified by num" optional="true" help="(-L)" /> + <param name="a" type="select" label="Normalize the score by the average size of two structures" help="(-a)"> + <option value="false" selected="true">Do not use this option</option> + <option value="true">Use this option</option> + </param> + <param name="b" type="select" label="Normalize the score by the minimum size of two structures" help="(-b)"> + <option value="false" selected="true">Do not use this option</option> + <option value="true">Use this option</option> + </param> + <param name="c" type="select" label="Normalize the score by the maximum size of two structures" help="(-c)"> + <option value="false" selected="true">Do not use this option</option> + <option value="true">Use this option</option> + </param> + </section> </inputs> <outputs> - <data name="output_apoc" format="data" /> + <data name="output_apoc" format="txt" /> </outputs> <tests> <test> @@ -253,6 +258,20 @@ ]]> </help> <citations> - <citation type="doi">doi:10.1093/bioinformatics/btt024</citation> + <citation type="bibtex"> + @article{Gao2013, + doi = {10.1093/bioinformatics/btt024}, + url = {http://dx.doi.org/10.1093/bioinformatics/btt024}, + year = {2013}, + month = {jan}, + publisher = {Oxford University Press ({OUP})}, + volume = {29}, + number = {5}, + pages = {597--604}, + author = {M. Gao and J. Skolnick}, + title = {{APoc}: large-scale identification of similar protein pockets}, + journal = {Bioinformatics} + } + </citation> </citations> </tool>