diff commet.xml @ 0:10e0e74c83af draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commet.xml	Fri Oct 20 03:14:44 2017 -0400
@@ -0,0 +1,108 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool profile="16.04" id="commet" name="Commet" version="24.7.14">
+    <description>COmpare Multiple METagenomes</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="24.7.14">commet</requirement>
+    </requirements>
+    <command><![CDATA[
+        #for $i, $set in enumerate( $sets )
+            echo "set${i}: ${ ','.join(['%s' % read for read in $set.reads]) }" >> commet_input_sets.txt &&
+        #end for
+        Commet.py
+        -k ${k}
+        -t ${t}
+        -l ${l}
+        -e ${e}
+        #if str( $options_advanced.options_advanced_selector ) == "advanced"
+            -m ${options_advanced.m}
+            -n ${options_advanced.n}
+        #end if
+        commet_input_sets.txt
+
+    ]]></command>
+
+    <inputs>
+        <!-- Input data files -->
+        <repeat name="sets" title="Read sets" min="1">
+            <param name="reads" type="data" multiple="true" format="fasta, fastq" label="Dataset" help="Accept fasta/fastq"/>
+        </repeat>
+        <param argument="-k" type="integer" label="Size of kmers" value="33" help="Set the length of used kmers." />
+        <param argument="-t" type="integer" label="Mini shared kmers" value="2" help="Minimal number of shared kmers." />
+        <param argument="-l" type="integer" label="Read mini length" value="66" help="Minimal length a read should have to be kept." />
+        <param argument="-e" type="float" label="Mini Shannon index" value="0" min="0" max="2.32" help="Minimal Shannon index a read should have to be kept." />
+        <conditional name="options_advanced">
+            <param name="options_advanced_selector" type="select" label="Reads filter options" help="By default, all reads are kept with no Ns limitation">
+                <option value="default" selected="true">default</option>
+                <option value="advanced">advanced</option>
+            </param>
+            <when value="default" />
+            <when value="advanced">
+                <param argument="-m" type="integer" value="-1" label="Maximum number of selected reads in sets" help="Maximum number of selected reads in sets. If a set is composed by 3 read files, and this option = 600, then the first 200 reads from each read file will be treated. (-1 = any)" />
+                <param argument="-n" type="integer" value="-1" label="Read maxi number of Ns" help="Maximal number of Ns a read should contain to be kept. (-1 = all)" />
+            </when>
+        </conditional>
+        <param name="normalized_outputs" label="Generate normalized files" type="boolean" checked="true"/>
+        <param name="plain_outputs" label="Generate plain files" type="boolean" checked="false"/>
+        <param name="percentage_outputs" label="Generate percentage files" type="boolean" checked="false"/>
+    </inputs>
+    <outputs>
+        <data format="csv" name="matrix_plain" from_work_dir="output_commet/matrix_plain.csv" label="Matrix plain with ${tool.name} on ${on_string}" >
+            <filter>plain_outputs</filter>
+        </data>
+        <data format="csv" name="matrix_percentage" from_work_dir="output_commet/matrix_percentage.csv" label="Matrix percentage with ${tool.name} on ${on_string}" >
+            <filter>percentage_outputs</filter>
+        </data>
+        <data format="csv" name="matrix_normalized" from_work_dir="output_commet/matrix_normalized.csv" label="Matrix normalized with ${tool.name} on ${on_string}" >
+            <filter>normalized_outputs</filter>
+        </data>
+        <data format="png" name="dendrogram_normalized" from_work_dir="output_commet/dendrogram_normalized.png" label="Dendrogram ${tool.name} on ${on_string}" />
+        <data format="png" name="heatmap_normalized" from_work_dir="output_commet/heatmap_normalized.png" label="Heatmap normalized with ${tool.name} on ${on_string}" >
+            <filter>normalized_outputs</filter>
+        </data>
+        <data format="png" name="heatmap_percentage" from_work_dir="output_commet/heatmap_percentage.png" label="Heatmap percentage with ${tool.name} on ${on_string}" >
+            <filter>percentage_outputs</filter>
+        </data>
+        <data format="png" name="heatmap_plain" from_work_dir="output_commet/heatmap_plain.png" label="Heatmap Plain with ${tool.name} on ${on_string}" >
+            <filter>plain_outputs</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_type" value="list" />
+            <repeat name="sets">
+                <param name="reads" value="commet/A.fa" ftype="fasta" />
+            </repeat>
+            <repeat name="sets">
+                <param name="reads" value="commet/B.fa,commet/C.fa" ftype="fasta" />
+            </repeat>
+            <repeat name="sets">
+                <param name="reads" value="commet/D.fa" ftype="fasta" />
+            </repeat>
+            <param name="plain_outputs" value="True"/>
+            <output name="dendrogram_normalized" file="commet/dendrogram.png" compare="sim_size" delta="10000"/>
+            <output name="matrix_plain" file="commet/matrix_plain.csv"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**Description**
+
+COMMET (COmpare Multiple METagenomes”) provides a global similarity overview between all datasets of a large metagenomic project.
+
+Directly from non-assembled reads, all against all comparisons are performed through an efficient indexing strategy. Then, results are stored as bit vectors, a compressed representation of read files, that can be used to further combine read subsets by common logical operations. Finally, COMMET computes a clusterization of metagenomic datasets, which is visualized by dendrogram and heatmaps.
+
+
+-------
+
+**Web site**
+
+http://colibread.inria.fr/commet/
+
+    ]]></help>
+    <expand macro="citations">
+        <citation type="doi">10.1186/1471-2105-13-S19-S10</citation>
+    </expand>
+</tool>