comparison SNP_density/calculateSlidingWindowsSNPdensitiesFromHapMap_wrapper.xml @ 4:10627af23f10 draft

planemo upload

3:345f88a8f483

<tool id="sniplay_density" name="SNP density" version="1.2.0">
    
    <!-- [REQUIRED] Tool description displayed after the tool name -->
    <description> Calculate SNP densities along chromosome from HapMap</description>
    
    <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
    <requirements>
        <requirement type="binary">perl</requirement>
    </requirements>
    
    <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
    <version_command>
<!--
        tool_binary -v
-->

    
    <!-- [REQUIRED] The command to execute -->
    <command interpreter="bash">
	calculateSlidingWindowsSNPdensitiesFromHapmap.sh $filein $fileout $fileout_bysample $step
    </command>
   
    <!-- [REQUIRED] Input files and tool parameters -->
    <inputs>
	<param name="filein" type="data" format="txt" optional="false" label="Hapmap input" />
	<param name="step" type="integer" value="200000" label="Step" help="Step in bp"/>
	<param name="fileout_label" type="text" value="densities" label="Output name" help="Output name for tabular files" />

    <!-- [REQUIRED] Output files -->
    <outputs>
	<data name="fileout" type="data" format="tabular" label="${fileout_label}" />
	<data name="fileout_bysample" type="data" format="tabular" label="${fileout_label}.by_sample" />
    </outputs>
    
    <!-- [STRONGLY RECOMMANDED] Exit code rules -->
    <stdio>
        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
        <exit_code range="1:" level="fatal" />
    </stdio>
    
    <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
    <tests>
        <!-- [HELP] Test files have to be in the ~/test-data directory -->
<!--
        <test>
         <param name="input" value="input_test.txt" />
         <output name="output" file="output_test.txt" />
        </test>
-->
        <!-- [HELP] Multiple tests can be defined with different parameters -->
<!--
        <test>
        </test>
-->

4:10627af23f10

<tool id="sniplay_density" name="SNP density" version="1.3.0">
    
    <!-- [REQUIRED] Tool description displayed after the tool name -->
    <description> Calculate SNP densities along chromosome from HapMap</description>
    
    <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
    <requirements>
        <requirement type="binary">perl</requirement>
    </requirements>
    
    <!-- [STRONGLY RECOMMANDED] Exit code rules -->
    <stdio>
        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
      <exit_code range="1:" level="fatal" />
    </stdio>

    <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
    <version_command>
<!--
        tool_binary -v
-->

    
    <!-- [REQUIRED] The command to execute -->
    <command interpreter="bash">
	calculateSlidingWindowsSNPdensitiesFromHapmap.sh $filein $fileout $fileout_bysample $step
    </command>

    <!-- [REQUIRED] Input files and tool parameters -->
    <inputs>
	<param name="filein" type="data" format="txt" optional="false" label="Hapmap input" />
	<param name="step" type="integer" value="200000" label="Step" help="Step in bp"/>
	<param name="fileout_label" type="text" value="densities" label="Output name" help="Output name for tabular files" />

    <!-- [REQUIRED] Output files -->
    <outputs>
	<data name="fileout" type="data" format="tabular" label="${fileout_label}" />
	<data name="fileout_bysample" type="data" format="tabular" label="${fileout_label}.by_sample" />
    </outputs>

    <tests>
        <test> 
         <param name="filein" value="SNPden-hapmap" />
         <param name="step" value="200000" />
         <output name="fileout" file="SNPden-result.txt" />
         <output name="fileout_bysample" file="SNPden-result_bysample.txt" />
        </test>
        <!-- [HELP] Multiple tests can be defined with different parameters -->
<!--
        <test>
        </test>
-->