Mercurial > repos > marpiech > norwich_tools_dock
diff apoc.xml @ 1:dc6fb5c5d4c8 draft
planemo upload commit 489ad526806f22eefcb73e8d8efe44d648e8185e
| author | marpiech |
|---|---|
| date | Mon, 12 Sep 2016 06:00:34 -0400 |
| parents | |
| children | 958fa7ba4715 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/apoc.xml Mon Sep 12 06:00:34 2016 -0400 @@ -0,0 +1,258 @@ +<tool id="apoc" name="APoc" version="1.0"> + <description>Large-scale identification of similar protein pockets</description> + <stdio> + <exit_code range="1:" /> + </stdio> + <command> + <![CDATA[ + #if $templates_source.template_source_select=="list"# + #for $i, $s in enumerate( $templates_source.template )# + echo ${s.input.file_name} >> templates_path ; + #end for# + paste -d "\t" templates_path $templates_source.lt | awk '{print $1"\t"$3}' > templates_list; + #end if# + + #if $query_source.query_source_select=="list"# + #for $i, $s in enumerate( $query_source.query )# + echo ${s.input.file_name} >> queries_path ; + #end for# + paste -d "\t" queries_path $query_source.lq | awk '{print $1"\t"$3}' > queries_list; + #end if# + + $__tool_directory__/tools/apoc/apoc + -fa $fa + -pvol $pvol + -plen $plen + #if $sod=="true" + -sod + #end if + -v $v + -m $m + #if $L + -L $L + #end if + #if $a=="true" + -a + #end if + #if $b=="true" + -b + #end if + #if $c=="true" + -c + #end if + + #if $templates_source.template_source_select=="list" + -lt templates_list + #else + #if $templates_source.pt + -pt $templates_source.pt + #end if + $templates_source.pdbfile1 + #end if + + #if $query_source.query_source_select=="list" + -lq queries_list + #else + #if $query_source.pq + -pq $query_source.pq + #end if + $query_source.pdbfile2 + #end if + > $output_apoc + ]]> + </command> + <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> + </param> + <when value="pdbfile"> + <param name="pdbfile1" type="data" format="pdb" label="First (template) structure for comparison" help="(pdbfile1)" /> + <param name="pt" type="text" label="Names of pockets in the first (template) structure for comparison" optional="true" help="(-pt)" /> + </when> + <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" /> + </repeat> + </when> + </conditional> + <conditional name="query_source"> + <param name="query_source_select" type="select" label="Chose query source: pdb file or file with list of queries"> + <option value="pdbfile">pdb file </option> + <option value="list">file with list of queries</option> + </param> + <when value="pdbfile"> + <param name="pdbfile2" type="data" format="pdb" label="Second (query) structure for comparison" help="(pdbfile2)" /> + <param name="pq" type="text" label="Names of pockets in the second (query) structure for comparison" optional="true" help="(-pq)" /> + </when> + <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" /> + </repeat> + </when> + </conditional> + <param name="fa" type="select" label="Global structure alignment" help="(-fa)"> + <option value="1" selected="true">enable </option> + <option value="0">disable </option> + </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> + </inputs> + <outputs> + <data name="output_apoc" format="data" /> + </outputs> + <tests> + <test> + <param name="template_source_select" value="pdbfile" /> + <param name="pdbfile1" value="apoc/1ha3A.pdb" ftype="pdb" /> + <param name="query_source_select" value="pdbfile" /> + <param name="pdbfile2" value="apoc/3ec1A.pdb" ftype="pdb" /> + <output name="output_apoc"> + <assert_contents> + <has_text_matching expression="PDB\s*files\s*loaded" /> + </assert_contents> + </output> + </test> + <test> + <param name="template_source_select" value="list" /> + <param name="lt" value="apoc/templ.lst" /> + <param name="template_0|input" value="apoc/1ha3A.pdb" ftype="pdb" /> + <param name="template_1|input" value="apoc/3ec1A.pdb" ftype="pdb" /> + <param name="template_2|input" value="apoc/1yr8A.pdb" ftype="pdb" /> + <param name="query_source_select" value="pdbfile" /> + <param name="pdbfile2" value="apoc/1yr8A.pdb" ftype="pdb" /> + <output name="output_apoc"> + <assert_contents> + <has_text_matching expression="PDB\s*files\s*loaded" /> + </assert_contents> + </output> + </test> + <test> + <param name="template_source_select" value="list" /> + <param name="lt" value="apoc/templ.lst" /> + <param name="template_0|input" value="apoc/1ha3A.pdb" ftype="pdb" /> + <param name="template_1|input" value="apoc/3ec1A.pdb" ftype="pdb" /> + <param name="template_2|input" value="apoc/1yr8A.pdb" ftype="pdb" /> + <param name="query_source_select" value="pdbfile" /> + <param name="pdbfile2" value="apoc/1ha3A.pdb" ftype="pdb" /> + <param name="pq" value="1ha3_GDP_A_406" /> + <output name="output_apoc"> + <assert_contents> + <has_text_matching expression="PDB\s*files\s*loaded" /> + </assert_contents> + </output> + </test> + <test> + <param name="template_source_select" value="list" /> + <param name="lt" value="apoc/templ.lst" /> + <param name="template_0|input" value="apoc/1ha3A.pdb" ftype="pdb" /> + <param name="template_1|input" value="apoc/3ec1A.pdb" ftype="pdb" /> + <param name="template_2|input" value="apoc/1yr8A.pdb" ftype="pdb" /> + <param name="query_source_select" value="list" /> + <param name="lq" value="apoc/query.lst" /> + <param name="query_0|input" value="apoc/3ec1A.pdb" ftype="pdb" /> + <output name="output_apoc"> + <assert_contents> + <has_text_matching expression="PDB\s*files\s*loaded" /> + </assert_contents> + </output> + </test> + </tests> + <help> + <![CDATA[ +************* +Description +************* + +APoc may be used to compare two pockets, a pocket against a set of pockets, or +all-against-all between two sets of pockets. If you supply two structures to compare, +the first structure is the template and the second structure is the query (or target). + +For each pair of structures, the program first performs a global structural comparison in +sequential order using a standard TM-align algoritm. One may elect to bypass the global alignment +to accelerate comparison. If no pocket found in the pdb structures, the program becomes a normal +TM-align or stop if one chooses to bypass the global alignment. If there are pockets detected +in the input files, it will compare pockets in sequential-order-independent manner by default. + +The ouput is arranged in pairs of structures compared. For each pair, the first alignment is the +global alignment, followed by all-againat-all alignment of selected pockets. If you want a concise +output without detailed alignment, add the "-v 0" option. + +****** +Help +****** + + Usage: apoc <options> pdbfile1 pdbfile2 + + **Input options** + + --fa <num> + Global structure alignment: 1 - enable (default), 0 - disable. + --lt <file> + Provide a list of templates to compare in a file. + --lq <file> + Provide a list of queries (targets) to compare in a file. + --pt <str1,str2,...> + Names of pockets in the first (template) structure for comparison. + --pq <str1,str2,...> + Names of pockets in the second (query) structure for comparison. + --pvol <num> + Minimal pocket volume in grid points. Default 100 + --plen <num> + Minimal number of pocket residues. Default 10 + + **Alignment options** + + --sod + Restrict to sequence-order-dependent alignment. Default no restriction. + --v + Alignment printout: 0 - none, 1 - concise, 2 - detailed (default). + + **Scoring options** + + --m <str> + Similarity scoring metric: tm (TM-score), ps (PS-score, default). + --L <num> + Normalize the score with a fixed length specified by num. + --a + Normalize the score by the average size of two structures. + --b + Normalize the score by the minimum size of two structures. + --c + Normalize the score by the maximum size of two structures. + + ]]> + </help> + <citations> + <citation type="doi">doi:10.1093/bioinformatics/btt024</citation> + </citations> +</tool>