annotate apoc.xml @ 2:958fa7ba4715 draft

planemo upload commit 489ad526806f22eefcb73e8d8efe44d648e8185e-dirty

<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 $alignment_option.sod=="true"
                                            -sod
                                            #end if
                                            -v $alignment_option.v

                                            -m $scoring_option.m
                                            #if $scoring_option.L
                                            -L $scoring_option.L
                                            #end if
                                            #if $scoring_option.a=="true"
                                            -a
                                            #end if
                                            #if $scoring_option.b=="true"
                                            -b
                                            #end if
                                            #if $scoring_option.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" help="load all pdb files in the same order as in the list of templates" />
                </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" help="load all pdb files in the same order as in the list of queries" />
                </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)" />
        <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="txt" />
    </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="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>