diff pep_match.xml @ 0:c42da0e5a671 draft

"planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"

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+++ b/pep_match.xml	Fri Dec 10 10:35:58 2021 +0000
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+<tool id="peptimapper_pep_match" name="PepMatch" version="2.0">
+    <description>align PSTs on sequence and cluster hits</description>
+    <requirements>
+        <container type="docker">dockerprotim/peptimapper</container>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+LXRunPepMatch -D $D -t $t -T $T -d $d '$fastafile' '$tagsfile' &&
+mv '${tagsfile}'.\$(basename '${fastafile}').trans.${D}.hit ${hitsfile} &&
+mv '${tagsfile}'.\$(basename '${fastafile}').trans.${D}.hit.${t}.${T}.${d}.clust '${clustersfile}'
+    ]]></command>
+    <inputs>
+        <param name="tagsfile" type="data" format="txt" label="PSTs file (Text)" help="Peptide sequence tags file generated by PepnovoTag" />
+        <param name="fastafile" type="data" format="fasta" label="Chromosome file (Fasta)" help="Chromosome file" />
+
+        <param name="D" type="select" label="Mass tolerance" help="uma">
+            <option value="0.5" selected="selected">0.5</option>
+            <option value="0.25">0.25</option>
+            <option value="0.025">0.025</option>
+            <option value="0.0025">0.0025</option>
+            <option value="0">0</option>
+        </param>
+
+        <param name="t" type="select" label="Min. hits" help="Minimal hits number per cluster">
+            <option value="2" selected="selected">2</option>
+            <option value="3">3</option>
+            <option value="4">4</option>
+        </param>
+
+        <param name="T" type="select" label="Min. peptides" help="Minimal peptides number per cluster">
+            <option value="2" selected="selected">2</option>
+            <option value="3">3</option>
+            <option value="4">4</option>
+        </param>
+
+        <param name="d" type="select" label="Distance" help="Maximum distance between two hits to be clustered">
+            <option value="500">500</option>
+            <option value="1000">1000</option>
+            <option value="2000">2000</option>
+            <option value="5000" selected="selected">5000</option>
+            <option value="10000">10000</option>
+            <option value="15000">15000</option>
+            <option value="20000">20000</option>
+            <option value="50000">50000</option>
+            <option value="80000">80000</option>
+            <option value="100000">100000</option>
+            <option value="120000">120000</option>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data format="txt" name="hitsfile" label="${tagsfile.element_identifier}.${fastafile.element_identifier}.${D}.hit"/>
+        <data format="txt" name="clustersfile" label="${tagsfile.element_identifier}.${fastafile.element_identifier}.${D}.hit.${t}.${T}.${d}.clust"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="tagsfile" value="pepnovotag/sample_02.mgf.3.5.tag"/>
+            <param name="fastafile" value="pepmatch/Nuc_genome_small.fasta"/>
+            <param name="D" value="0.5"/>
+            <param name="t" value="2"/>
+            <param name="T" value="2"/>
+            <param name="d" value="5000"/>
+            <output name="hitsfile" file="pepmatch/sample_02.mgf.3.5.tag.Nuc_genome_small.fasta.0.5.hit"/>
+            <output name="clustersfile" file="pepmatch/sample_02.mgf.3.5.tag.Nuc_genome_small.fasta.0.5.hit.2.2.5000.clust"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+**Description**
+
+PepMatch : run LXRunPepMatch from peptimapper docker. It translates chromosome sequence into six-frame translations, aligns PSTs and clusters hits. PepMatch outputs are a hits (or PST locations) file on the genome and a clusters (hits list per cluster) file. PepMatch clusters results are compatible with ClustQualify and ClustToGff to be annotated and analysed into a genome viewer.
+
+It is based on the PepLine software developed by Ferro and collaborators
+Ferro, M., Tardif, M., Reguer, E., Cahuzac, R., Bruley, C., Vermat, T., Nugues, E., Vigouroux, M., Vandenbrouck, Y., Garin, J. & Viari, A. 2008. PepLine: a software pipeline for high-throughput direct mapping of tandem mass spectrometry data on genomic sequences. J Proteome Res 7:1873-83.
+
+**Integrated by**
+
+Laetitia Guillot Cloarec
+PROTIM Biogenouest proteomics Core Facility, Rennes
+May,2016
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+            @misc{renameTODO,
+            author = {Protim Core facility},
+            year = {2016},
+            title = {PepMatch},
+            url = {protim.eu},
+            }
+        </citation>
+    </citations>
+</tool>