annotate apoc.xml @ 0:67d2a6f3b4e3 draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/apoc/ commit d25418e6fe5eddd1a1cc68979e5898fb224feffe

<tool id="apoc" name="APoc" version="1.0">
    <description>Large-scale identification of similar protein pockets</description>
    <requirements>
        <requirement type="package" version="1b16">apoc</requirement>
    </requirements>
    <command detect_errors="exit_code"><![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#

apoc
-fa $fa
-pvol $pvol
-plen $plen
$alignment_option.sod
-v $alignment_option.v
-m $scoring_option.m
#if str($scoring_option.L)
    -L $scoring_option.L
#end if
$scoring_option.a
$scoring_option.b
$scoring_option.c

#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" />
                <param argument="-pt" type="text" label="Names of pockets in the first (template) structure for comparison" optional="true" />
            </when>
            <when value="list">
                <param argument="-lt" type="data" format="data" label="List of templates to compare in a file" />
                <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" />
                <param argument="-pq" type="text" optional="true" label="Names of pockets in the second (query) structure for comparison" />
            </when>
            <when value="list">
                <param argument="-lq" type="data" format="data" label="List of queries (targets) to compare in a file." />
                <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 argument="-fa" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Global structure alignment" />
        <param argument="-pvol" type="integer" value="1000" label="Minimal pocket volume in grid points" />
        <param argument="-plen" type="integer" value="10" label="Minimal number of pocket residues" />
        <section name="alignment_option" title="Alignment option">
            <param argument="-sod" type="boolean" truevalue="-sod" falsevalue="" label="Restrict to sequence-order-dependent alignment" />
            <param argument="-v" type="select" label="Restrict to sequence-order-dependent alignment" >
                <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 argument="-m" type="select" label="Similarity scoring metric" >
                <option value="tm">TM-score</option>
                <option value="ps" selected="true">PS-score</option>
            </param>
            <param argument="-L" type="integer" optional="true" label="Normalize the score with this fixed length" />
            <param argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Normalize the score by the average size of two structures" />
            <param argument="-b" type="boolean" truevalue="-b" falsevalue="" label="Normalize the score by the minimum size of two structures" />
            <param argument="-c" type="boolean" truevalue="-c" falsevalue="" label="Normalize the score by the maximum size of two structures" />
        </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>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btt024</citation>
    </citations>
</tool>