comparison samtools_phase.xml @ 3:c21cb56fbbbc draft

planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

2:2656247b5253

<tool id="samtools_phase" name="Call and phase" version="1.0.2">
    <description>heterozygous SNPs</description>
    <requirements>
        <requirement type="package" version="1.1">samtools</requirement>
    </requirements>
    <command>samtools phase -b "phase_wrapper"
        #if str($option_set.option_sets) == 'advanced':
            ${option_set.ignore_chimeras}
            -k $option_set.block_length
            -q $option_set.min_het

        #else
            -k 13 -q 37 -Q 13 -D 256
        #end if
        "$input_bam" > "$phase_sets"
    </command>
    <stdio>
        <exit_code range="1:" level="fatal" description="Error" />
    </stdio>
    <inputs>
        <param format="bam" name="input_bam" type="data" label="Select dataset to phase"/>
        <conditional name="option_set">
            <param name="option_sets" type="select" label="Phase parameters">
                <option value="default">Use defaults</option>

   * - -A
     - BOOLEAN
     - Drop reads with ambiguous phase
     - *off*

------

**Citation**

For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_


If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*

        </help>
</tool>

3:c21cb56fbbbc

<tool id="samtools_phase" name="Call and phase" version="2.0">
    <description>heterozygous SNPs</description>
    <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"></expand>
  <expand macro="stdio"></expand>
  <expand macro="version_command"></expand>
    <command>samtools phase -b "phase_wrapper"
        #if str($option_set.option_sets) == 'advanced':
            ${option_set.ignore_chimeras}
            -k $option_set.block_length
            -q $option_set.min_het

        #else
            -k 13 -q 37 -Q 13 -D 256
        #end if
        "$input_bam" > "$phase_sets"
    </command>
    <inputs>
        <param format="bam" name="input_bam" type="data" label="Select dataset to phase"/>
        <conditional name="option_set">
            <param name="option_sets" type="select" label="Phase parameters">
                <option value="default">Use defaults</option>

   * - -A
     - BOOLEAN
     - Drop reads with ambiguous phase
     - *off*

    </help>
    <expand macro="citations"></expand>
</tool>