comparison fasta_filter_region.xml @ 0:bc23da9d464c draft default tip

planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4

0:bc23da9d464c

<tool id="fasta_filter_region_wrapper" name="Filter region" version="0.1">
  <description></description>
  <requirements>
	<requirement type="package" version="1.78">biopython</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" level="fatal" />
  </stdio>
  <version_command>$__tool_directory__/fasta_filter_to_region.py -v</version_command>
  <command>
    $__tool_directory__/fasta_filter_to_region.py
	-o '$output'
	'$fasta'
	#for $reg in $regions.split(" ")
	 '$reg'
	#end for
  </command>
  <inputs>
    <param name="fasta" type="data" format="fasta" label="Database to filter on fasta" help="FASTA format" />
	<param name="regions" type="text" value="" optional="false" size="4X50"
		   label="List of region to conserved in format accession:start-stop"
		   help="Separated each regions by a space" />
  </inputs>
  <outputs>
    <data name="output" format="fasta" label="${tool.name} on ${on_string}: fasta" />
  </outputs>
  <tests>
	<test expect_num_outputs="1">
      <param name="fasta" value="input.fasta" />
      <param name="regions" value="NODE_1_length_344587_cov_27.773165:10-190" />
      <output name="output" file="filter_region.fasta" ftype="fasta" />
    </test>
  </tests>
  <help>
**What it does**

Filter a fasta file based on regions.

**Examples**

CP000822.1:458-1689 

NODE_1_length_721117_cov_11.496472:14500-18320

**Citation et licences**

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

  </help>
  <citations>
  </citations>
</tool>