diff quast.xml @ 0:736d51130b41 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit d0e7095e03f99c80d6cc8f7a2bfb3c5bef33df09

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/quast.xml	Tue Sep 13 14:43:54 2016 -0400
@@ -0,0 +1,129 @@
+<tool id="quast" name="Quast" version="4.1" >
+    <description>Genome assembly Quality</description>
+    <requirements>
+        <requirement type="package" version="4.1">quast</requirement>
+    </requirements>
+    <stdio>
+        <regex match="ERROR! exception caught!"
+            source="both"
+            level="fatal"
+            description="Something went wrong. Check the following errors : No labels..." />
+    </stdio>
+    <command>
+    <![CDATA[
+        quast
+        -o outputdir
+        #if $gene_selection == "eukaryote":
+            --eukaryote
+        #else if $gene_selection == "metagenes":
+            --meta
+        #end if
+        #if $input_ref:
+            -R '$input_ref'
+            #if $input_operon:
+                -O '$input_operon'
+            #end if
+            #if $annot:
+                -G '$annot'
+            #end if
+        #end if
+        #if $input_size:
+            --est-ref-size $input_size
+        #end if
+        --min-contig $min_contig
+        --contig-thresholds $threshold_contig
+        #for $k in $files:
+            #if $k.type_file == "scaffold":
+                -s
+            #end if
+        $k.input
+        #end for
+        &&
+        mv outputdir/report.txt '$quast_out' &&
+        mv outputdir/report.tsv '$quast_tsv' &&
+        mv outputdir/report.tex '$quast_tex' &&
+        mv outputdir/icarus_viewers/contig_size_viewer.html '$icarus' &&
+        mv outputdir/report.html '$report_html' 
+    ]]>
+    </command>
+    <inputs>
+        <repeat name="files" title="Input assembly files" min="1">
+            <param type="data" format="fasta" name="input" label="Contigs/scaffolds output file"/>
+            <param name="type_file" type="select" label="Type of data">
+                <option value="contig">Contig</option>
+                <option value="scaffold">Scaffold</option>
+            </param>
+        </repeat>
+        <param name="input_size" type="integer" label="Size of reference genome" optional="True"  argument="--est-ref-size"
+            help="Estimated reference genome size (in bp) for computing NGx statistics, if known. This value will be used only if a reference genome file is not specified "/>
+        <param name="input_ref" type="data" format="fasta"  label="Reference File" optional="True"  argument="-R"
+            help="Many metrics can't be evaluated without a reference. If this is omitted, QUAST will only report the metrics that can be evaluated without a reference."/>
+        <param name="annot" type="data" format="txt" label="Gene Annotations" optional="True" argument="-G"
+            help="File with gene positions in the reference genome. "/>
+        <param name="input_operon" type="data" format="txt" label="Operon Annotations"  optional="True" argument="-O"
+            help="File with operon positions in the reference genome"/>
+        <param name="gene_selection" type="select" label="Type of organism">
+            <option value="prokaryotes">Prokaryotes</option>
+            <option value="eukaryote">Eukaryote</option>
+            <option value="metagenes">Metagenomes</option>
+        </param>
+        <param name="min_contig" type="integer" value="500" label="Lower Threshold"  argument="--min-contig"
+            help="Set the lower threshold for a contig length. Shorter contigs won't be taken into account (default is 500)"/>
+        <param name="threshold_contig" type="text" value="0,1000" label="Thresholds" argument="--contig-thresholds"
+            help="Set the thresholds for contig length. Comma-separated list of contig length thresholds.(default is 0,1000)"/>
+    </inputs>
+    <outputs>
+        <data format="txt" name="quast_out" label="Quast report.txt" from_work_dir="Quast_report.txt"/>
+        <data format="tsv" name="quast_tsv" label="Quast report.tsv" from_work_dir="Quast_report.tsv"/>
+        <data format="tex" name="quast_tex" label="Quast report.tex" from_work_dir="Quast_report.tex"/>
+        <data format="html" name="icarus" label="Icarus Contig size viewer" from_work_dir="Icarus.html"/>
+        <data format="html" name="report_html" label="Quast report.html" from_work_dir="Quast_report.html"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="contigs_1.fasta"/>
+            <param name="input.type_file" value="contig"/>
+            <param name="gene_selection" value="prokaryotes"/>
+            <output name="quast_tsv" file="Quast_report.tsv" lines_diff="4"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**Description**
+
+Galaxy tool wrapper for the QUAST tool. Quast stands for QUality ASsessment Tool. It evaluates genome assemblies by computing various metrics.
+
+-----
+
+**Inputs and Outputs**
+
+- Input:
+    + The tool accepts assemblies and references in FASTA format.
+    + The tool accepts annotation and operon files in:
+        + GFF, versions 2 and 3 (note: feature/type field should be either "gene" or "operon")
+        + the format used by NCBI for genes ("Summary (text)");
+        + four tab-separated columns: sequence name, gene/operon id, start position, end position
+
+- Output:
+    + An assessment summary in plain text format
+    + An assessment summary in tabulation separated values format
+    + An assessment summary in LateX format
+    + An assessment summary in HTML format
+    + An HTML view of contig sizes wit Icarus
+
+
+    ]]>
+    </help>
+
+    <citations>
+        <citation type="bibtex">@ARTICLE{a1,
+            author = {Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler},
+            title = {QUAST: quality assessment tool for genomce assemblies, Bioinformatics (2013) 29 (8): 1072-1075}
+        }</citation>
+        <citation type="bibtex">@misc{quast41,
+            title = {{Quast} v4.1},
+            howpublished = {http://bioinf.spbau.ru/quast},
+            note = {Released May 2016}}
+        }</citation>
+    </citations>
+</tool>