view panisa.xml @ 0:349c2fbd38a0 draft default tip

"planemo upload for repository https://github.com/bvalot/panISa commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb"

<tool id="panisa2_wrapper" name="PanISa: IS search" version="0.1.6">
  <description>Search integrative element (IS) insertion on a genome using BAM alignment</description>
  <requirements>
	<requirement type="package" version="0.1.6">panisa</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" level="fatal" />
  </stdio>
  <version_command>panISa.py -v</version_command>
  <command>
    panISa.py
    #if str($quality)
      -q $quality
    #end if
    #if str($minimun)
      -m $minimun
    #end if
    #if str($size)
      -s $size
    #end if
    #if str($percentage)
	  -p $percentage
    #end if
	'$bam' > '$output'
  </command>
  <inputs>
    <param name="bam" type="data"
		   format="bam"
		   label="Alignment result"
		   help="Bam format" />
	<param name="quality" type="integer" value="20"
		   optional="true"
		   label="Minimun alignment quality value to conserve a clipped" />
	<param name="minimun" type="integer" value="5"
		   optional="true"
		   label="Minimun number of clipped reads to look at IS on a position" />
	<param name="size" type="integer" value="20"
		   optional="true"
		   label="Maximun size of direct repeat region" />
	<param name="percentage" type="float" value="0.8"
		   optional="true"
		   label="Minimum percentage of same base to create consensus" />
  </inputs>
  <outputs>
    <data name="output" format="tabular" label="panISa on ${bam.name}">
	  <!-- <actions> -->
      <!--   <action name="column_names" type="metadata" default="Chromosome,End position,End clipped reads,Direct repeats,Start position,Start clipped reads,Inverted repeats,Left sequence,Right sequence" /> -->
      <!-- </actions> -->
	</data>
  </outputs>
  <tests>
	<test expect_num_outputs="1">
      <param name="bam" value="input.bam" />
      <output name="output" file="panisa.txt" ftype="tabular" />	  
	</test>
  </tests>
  <help>
**What it does**

Search integrative element (IS) insertion on a genome using BAM alignment.

**License and citation**

This Galaxy tool is Copyright © 2018 `B. Valot` and is released under the `GPL3 license`.

PanISa program was publised :

Treepong, P., Guyeux, C., Meunier, A., Couchoud, C., Hocquet, D. et Valot, B. (2018). PanISa : Ab initio detection of insertion sequences in bacterial genomes from short read sequence
data. Bioinformatics.
  </help>
  <citations>
	<citation type="doi">10.1093/bioinformatics/bty479</citation>
  </citations>
</tool>