comparison commet.xml @ 3:d085f995d556

remove prepare_commet and change/add packages

2:1478d48df8c7

<tool id="commet" name="commet" version="24.7.14">
  <description>COmpare Multiple METagenomes</description>
  <requirements>
    <requirement type="package" version="24.7.14">commet</requirement>
    <requirement type="package" version="2.15.0">R</requirement>
    <requirement type="package" version="0.9.3">ggplot2</requirement>
  </requirements>
<command interpreter="python">
commet.py
--input $input
-k $kmer
-t $minsharedkmer
-l $minlengthread
-e $minshannonindex
#if str( $options_advanced.options_advanced_selector ) == "advanced"

-n $options_advanced.maxn
#end if
--output $output
--output_vectors $output_vectors
--output_dendro $output_dendro
--output_logs $output_logs
--output_matrix $output_matrix
--output_heatmap1 $output_heatmap1
--output_heatmap2 $output_heatmap2
--output_heatmap3 $output_heatmap3
</command>

  <inputs>
	<!-- Input data files -->
	<param name="input" type="data" format="commet" label="Read sets" help="input read sets a line = a set composed by “set_name: read_file; read_file...“. Generate with Prepare commet tool" /> 
	<param name="kmer" type="integer" label="Size of kmers" value="33" help="Set the length of used kmers." />
	<param name="minsharedkmer" type="integer" label="Mini shared kmers" value="2" help="Minimal number of shared kmers." />
	<param name="minlengthread" type="integer" label="Read mini length" value="0" help="Minimal length a read should have to be kept." />
	<param name="minshannonindex" type="float" label="Mini Shannon index" value="0" help="Minimal Shannon index a read should have to be kept. Float in [0,2.32]" />
	<conditional name="options_advanced">

			<param name="maxreads" type="integer" value="600" 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" />
			<param name="maxn" type="integer" value="5" label="Read maxi number of Ns" help="Maximal number of Ns a read should contain to be kept." />
		</when>
	</conditional>
  </inputs>

  <outputs>
      <data format="txt" name="output" label="${tool.name} on ${on_string}: commet.log" />
      <data format="zip" name="output_vectors" label="${tool.name} on ${on_string}: vector.zip" />
      <data format="zip" name="output_logs" label="${tool.name} on ${on_string}: logs.zip" />
      <data format="png" name="output_dendro" label="${tool.name} on ${on_string}: dendrogram.png" />
      <data format="zip" name="output_matrix" label="${tool.name} on ${on_string}: matrix.zip" />
      <data format="png" name="output_heatmap1" label="${tool.name} on ${on_string}: heatmap_normalized.png" />
      <data format="png" name="output_heatmap2" label="${tool.name} on ${on_string}: heatmap_percentage.png" />
      <data format="png" name="output_heatmap3" label="${tool.name} on ${on_string}: heatmap_plain.png" />
  </outputs>
  <help>

**Description**

COMMET (COmpare Multiple METagenomes”) provides a global similarity overview between all datasets of a large metagenomic project.

3:d085f995d556

<tool id="commet" name="commet" version="24.7.14">
  <description>COmpare Multiple METagenomes</description>
  <requirements>
    <requirement type="package" version="24.7.14">commet</requirement>
    <requirement type="package" version="3.0.1">R</requirement>
  </requirements>
<command interpreter="python">
commet.py
#for $set in $sets
    --set ${set.setname}::${set.reads}
#end for
-k $kmer
-t $minsharedkmer
-l $minlengthread
-e $minshannonindex
#if str( $options_advanced.options_advanced_selector ) == "advanced"

-n $options_advanced.maxn
#end if
--output $output
--output_vectors $output_vectors
--output_dendro $output_dendro
--output_matrix $output_matrix
--output_heatmap1 $output_heatmap1
--output_heatmap2 $output_heatmap2
--output_heatmap3 $output_heatmap3
</command>

  <inputs>
	<!-- Input data files -->
        <repeat name="sets" title="Read sets" min="1">
            <param name="reads" type="data" multiple="true" format="fasta, fastq, fastq.gz" label="Dataset" help="Accept fasta/fastq/fastq.gz"/>
            <param name="setname" type="text" label="Set name" value="set_name" help="Please don't use spaces or special characters"/>
        </repeat>
	<param name="kmer" type="integer" label="Size of kmers" value="33" help="Set the length of used kmers." />
	<param name="minsharedkmer" type="integer" label="Mini shared kmers" value="2" help="Minimal number of shared kmers." />
	<param name="minlengthread" type="integer" label="Read mini length" value="0" help="Minimal length a read should have to be kept." />
	<param name="minshannonindex" type="float" label="Mini Shannon index" value="0" help="Minimal Shannon index a read should have to be kept. Float in [0,2.32]" />
	<conditional name="options_advanced">

			<param name="maxreads" type="integer" value="600" 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" />
			<param name="maxn" type="integer" value="5" label="Read maxi number of Ns" help="Maximal number of Ns a read should contain to be kept." />
		</when>
	</conditional>
  </inputs>
  <outputs>
      <data format="zip" name="output_vectors" label="${tool.name} on ${on_string}: vector.zip" />
      <data format="zip" name="output_logs" label="${tool.name} on ${on_string}: logs.zip" />
      <data format="png" name="output_dendro" label="${tool.name} on ${on_string}: dendrogram.png" />
      <data format="zip" name="output_matrix" label="${tool.name} on ${on_string}: matrix.zip" />
      <data format="png" name="output_heatmap1" label="${tool.name} on ${on_string}: heatmap_normalized.png" />
      <data format="png" name="output_heatmap2" label="${tool.name} on ${on_string}: heatmap_percentage.png" />
      <data format="png" name="output_heatmap3" label="${tool.name} on ${on_string}: heatmap_plain.png" />
  </outputs>
  <stdio>
    <exit_code range="1" level="fatal" description="Error in Commet execution" />
  </stdio>  
  <help>

**Description**

COMMET (COmpare Multiple METagenomes”) provides a global similarity overview between all datasets of a large metagenomic project.