view pfamscan.xml @ 0:e7541ea105da draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan commit c27a05e92e6e03545903dd2ff90976f8cab5ebf7

<tool id="pfamscan" name="PfamScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>search a FASTA sequence against a library of Pfam HMM</description>
    <macros>
        <token name="@TOOL_VERSION@">1.6</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">pfamscan</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">pfam_scan</requirement>
        <requirement type="package" version="3.3.2">hmmer</requirement>
    </requirements>
    <version_command>pfam_scan.pl --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        mkdir -p './pfam_files' &&
        ln -s '${pfam_library}' './pfam_files/Pfam-A.hmm' &&
        ln -s '${pfam_data}' './pfam_files/Pfam-A.hmm.dat' &&
        #if $active_sites.selector == 'true'
            ln -s '${active_sites.active_file}' './pfam_files/active_site.dat' &&
        #end if
        hmmpress './pfam_files/Pfam-A.hmm' &&
        pfam_scan.pl 
            -cpu \${GALAXY_SLOTS:-4}
            -fasta '${fasta}'
            -dir './pfam_files/'
            -outfile './output.tab'
            #if $advanced_options.e_seq
                -e_seq $advanced_options.e_seq
            #end if
            #if $advanced_options.e_dom
                -e_dom $advanced_options.e_dom
            #end if
            #if $advanced_options.b_seq
                -b_seq $advanced_options.b_seq
            #end if
            #if $advanced_options.b_dom
                -b_dom $advanced_options.b_dom
            #end if
            #if $active_sites.selector == 'true'
             -as
            #end if
            && tail -n +28 "./output.tab" > "./output_fixed.tab"
        ]]>
    </command>
    <inputs>
        <param argument="-fasta" type="data" format="fasta" label="Protein sequences FASTA file"/>
        <param name="pfam_library" type="data" format="hmm3" label="Pfam-A HMM library" help="Pfam-A HMMs in an HMM library searchable with the hmmscan program." />
        <param name="pfam_data" type="data" format="stockholm" label="Pfam-A HMM Stockholm file" help="Stockholm format is a multiple sequence alignment format used 
            by Pfam, Rfam and Dfam, to disseminate protein, RNA and DNA sequence alignments." />
        <conditional name="active_sites">
            <param name="selector" type="select" label="Predict active site residues" help="Predict active site residues for Pfam-A matches">
                <option value="false">Disabled</option>
                <option value="true" selected="true">Enabled</option>
            </param>
            <when value="false"/>
            <when value="true">
                <param name="active_file" type="data" format="txt" label="Active sites file" help="This file is required for predicting the active site residues." />
            </when>
        </conditional>
        <section name="advanced_options" title="Advanced options">
            <param argument="-e_seq" type="float" min="0" value=""  optional="true" label="Hmmscan evalue sequence cutoff" help="Specify hmmscan evalue sequence cutoff 
                for Pfam-A searches (default Pfam defined)" />
            <param argument="-e_dom" type="float" min="0" value="" optional="true" label="Hmmscan evalue domain cutoff" help="Specify hmmscan evalue domain cutoff for 
                Pfam-A searches (default Pfam defined)" />
            <param argument="-b_seq" type="float" min="0" value=""  optional="true" label="Hmmscan bit score sequence cutoff" help="Specify hmmscan bit score sequence 
                cutoff for Pfam-A searches (default Pfam defined)" />
            <param argument="-b_dom" type="float" min="0" value=""  optional="true" label="Hmmscan bit score domain cutoff" help="Specify hmmscan bit score domain cutoff 
                for Pfam-A searches (default Pfam defined)" />
            <param argument="-clan_overlap" type="boolean" truevalue="-clan_overlap" falsevalue="" checked="false" label="Clan overlap" help="Show overlapping hits within 
                clan member families (applies to Pfam-A families only)" />
            <param argument="-align" type="boolean" truevalue="-align" falsevalue="" checked="false" label="Show alignment" help="Show the HMM-sequence alignment for each match" />
        </section>
    </inputs>
    <outputs>
        <data name="output" format="tabular" from_work_dir="output_fixed.tab" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <!-- Test 01: Default parameters not active sites -->
        <test expect_num_outputs="1">
            <param name="fasta" value="sequences.fasta.gz"/>
            <param name="pfam_library" value="Pfam-A.hmm.gz"/>
            <param name="pfam_data" value="Pfam-A.hmm.dat.gz"/>
            <conditional name="active_sites">
                <param name="selector" value="false"/>
            </conditional>
            <output name="output" file="test01.tab" ftype="tabular"/>
        </test>
        <!-- Test 02: Default parameters: active sites -->
        <test expect_num_outputs="1">
            <param name="fasta" value="sequences.fasta.gz"/>
            <param name="pfam_library" value="Pfam-A.hmm.gz"/>
            <param name="pfam_data" value="Pfam-A.hmm.dat.gz"/>
            <conditional name="active_sites">
                <param name="selector" value="true"/>
                <param name="active_file" value="active_site.dat.gz"/>
            </conditional>
            <output name="output" file="test02.tab" ftype="tabular"/>
        </test>
        <!-- Test 03: Non default parameters: active sites -->
        <test expect_num_outputs="1">
            <param name="fasta" value="sequences.fasta.gz"/>
            <param name="pfam_library" value="Pfam-A.hmm.gz"/>
            <param name="pfam_data" value="Pfam-A.hmm.dat.gz"/>
            <section name="advanced_options">
                <param name="e_seq" value="1.2"/>
                <param name="e_dom" value="1.3"/>
                <param name="clan_overlap" value="true"/>
            </section>
            <conditional name="active_sites">
                <param name="selector" value="true"/>
                <param name="active_file" value="active_site.dat.gz"/>
            </conditional>
            <output name="output" file="test03.tab" ftype="tabular"/>
        </test>
        <!-- Test 04: Non default parameters: active sites -->
        <test expect_num_outputs="1">
            <param name="fasta" value="sequences.fasta.gz"/>
            <param name="pfam_library" value="Pfam-A.hmm.gz"/>
            <param name="pfam_data" value="Pfam-A.hmm.dat.gz"/>
            <section name="advanced_options">
                <param name="b_seq" value="1.4"/>
                <param name="b_dom" value="1.2"/>
                <param name="align" value="true"/>
            </section>
            <conditional name="active_sites">
                <param name="selector" value="true"/>
                <param name="active_file" value="active_site.dat.gz"/>
            </conditional>
            <output name="output" file="test04.tab" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**Purpose**

Search one or more sequences for matching Pfam domains. Depending on the user options, the script can also process the results such that overlaps between families belonging to the 
same clan are resolved and can predict active sites.

----

.. class:: infomark

**Required files**

To run PfamScan you will need to download the following files from the Pfam ftp site:

- Pfam-A HMMs in an HMM library searchable with the hmmscan program: `Pfam-A.hmm.gz <https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz>`_
- Pfam-A HMM Stockholm file associated with each HMM required for PfamScan: `Pfam-A.hmm.dat.gz <https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.dat.gz>`_
- Active sites: `active_sites.dat.gz <ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/active_site.dat.gz>`_

]]></help>
    <citations>
        <citation type="doi">10.1093/nar/gkt006</citation>
    </citations>
</tool>