comparison tools/clinod/clinod.xml @ 4:4d9a4a43861b draft

Uploaded v0.0.7, uses $GALAXY_SLOTS and embeds citation in tool XML.

3:6a9debe4b860

<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.5">
    <description>Find nucleolar localization signals (NoLSs) in protein sequences</description>
    <requirements>
        <requirement type="binary">java</requirement>
        <requirement type="package" version="1.3">clinod</requirement>
    </requirements>
    <command>
##The Galaxy Tool Shed installation should define $CLINOD to point at folder
##containing both clinod-1.3.jar and the batchman binary:
java -jar \$CLINOD/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t=2 -f=MEDIUM_TAB -nonols -clean_sequence
##I want the number of threads to be a Galaxy config option...
##TODO - Make the -clean_sequence argument a parameter?
    </command>
    <stdio>
        <!-- Assume anything other than zero is an error -->
        <exit_code range="1:" />

        <data name="tabular_file" format="tabular" label="NoD results" />
    </outputs>
    <tests>
        <test>
            <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
	    <output name="tabular_file" file="four_human_proteins.clinod-1.3.tabular" ftype="tabular" />
        </test>
    </tests>
    <help>

**What it does**

This wrapper is available to install into other Galaxy Instances via the Galaxy
Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clinod

    </help>
</tool>

4:4d9a4a43861b

<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.7">
    <description>Find nucleolar localization signals (NoLSs) in protein sequences</description>
    <requirements>
        <requirement type="binary">java</requirement>
        <requirement type="package" version="1.3">clinod</requirement>
    </requirements>
    <command>
##The Galaxy Tool Shed installation should define $CLINOD to point at folder
##containing both clinod-1.3.jar and the batchman binary:
java -jar \$CLINOD/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t="\$GALAXY_SLOTS" -f=MEDIUM_TAB -nonols -clean_sequence
##TODO - Make the -clean_sequence argument a parameter?
    </command>
    <stdio>
        <!-- Assume anything other than zero is an error -->
        <exit_code range="1:" />

        <data name="tabular_file" format="tabular" label="NoD results" />
    </outputs>
    <tests>
        <test>
            <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
            <output name="tabular_file" file="four_human_proteins.clinod-1.3.tabular" ftype="tabular" />
        </test>
    </tests>
    <help>

**What it does**

This wrapper is available to install into other Galaxy Instances via the Galaxy
Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clinod

    </help>
    <citations>
        <citation type="doi">10.7717/peerj.167</citation>
        <citation type="doi">10.1093/nar/gkq653</citation>
        <citation type="doi">10.1186/1471-2105-12-317</citation>
    </citations>
</tool>