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

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

<tool id="isfinder_search_wrapper" name="ISFinder search" version="0.1.6">
  <description>Search IS homology in ISFinder from panISa output</description>
  <requirements>
	<requirement type="package" version="0.1.6">panisa</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" level="fatal" />
  </stdio>  
  <version_command>ISFinder_search.py -v</version_command>
  <command>
    ISFinder_search.py
    -r ' '
    #if str($length)
      -l $length
    #end if
    #if str($identity)
      -i $identity
    #end if
    #if str($evalue)
	  -e $evalue
    #end if
    #if str($alignment)
	  -a $alignment
    #end if
	#for $panisa in $panisa_list:
        #if $panisa:
            '$panisa'
        #end if
    #end for
	#for $panisa in $panisa_list:
        #if $panisa:
            | sed -e "~s/`echo $panisa.file_name | sed -e
			'~s/.*\///'`/$panisa.name.replace('panISa on ', '')/"
        #end if
	#end for
	> '$output'
	2> /dev/null
  </command>
  <inputs>
    <param name="panisa_list" type="data"
		   format="tabular" multiple="true"
		   label="Panisa result to merge"
		   help="Panisa output in tabular format" />
	<param name="length" type="integer" value="30"
		   optional="true"
		   label="Length of the IRR-IRL search" />
	<param name="identity" type="integer" value="90"
		   optional="true" min="0" max="100"
		   label="Percentage of expected identity" />
	<param name="evalue" type="float" value="0.001"
		   optional="true"
		   label="Expected max evalue" />
	<param name="alignment" type="integer" value="80"
		   optional="true" min="0" max="100"
		   label="Percentage of expected coverage" />	
  </inputs>
  <outputs>
    <data name="output" format="tabular" label="${tool.name} on	${on_string}">
	  <!-- <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="panisa_list" ftype="tabular" value="panisa.txt" />
      <output name="output" file="isfinder.txt" ftype="tabular" />	  
	</test>
  </tests>
  <help>
**What it does**

Automate search integrative element (IS) homology in ISFinder from panISa output.

**License and citation**

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

PanISa program was publised recently:

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>