view plink.xml @ 3:50f56c93c168 draft default tip

planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry/galaxy-tools/plink commit 5bc9005790b78aabb615f559f31ee71c714c7072

<?xml version="1.0"?>
<tool id="plink" name="PLINK" version="@TOOL_VERSION@+galaxy0">
  <description><![CDATA[
      PLINK is a free, open-source whole genome association analysis toolset, 
      designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
   ]]>  
   </description>
  <macros>
    <token name="@TOOL_VERSION@">1.90b4</token>
  </macros>

   <requirements>
    <requirement type="package" version="@TOOL_VERSION@">plink</requirement>
  </requirements>
        
  <command detect_errors="exit_code"><![CDATA[
    ln -s '${input_bed_file}' input_file.bed &&
    ln -s '${input_bim_file}' input_file.bim &&
    ln -s '${input_fam_file}' input_file.fam &&
    mkdir output &&
    for i in {1..${chr_num}};
    do 
      plink 
      --noweb 
      --bfile input_file 
      --chr \$i 
      --make-bed 
      --out output/input_file_chr\$i;
    done;
    
    ]]>                                                                                                                 
  </command>
        
  <inputs>
    <param name="input_bed_file" type="data" format="binary" label="Select the bed file"/> 
    <param name="input_bim_file" type="data" format="bim" label="Select the bim file"/> 
    <param name="input_fam_file" type="data" format="fam" label="Select the fam file"/> 
    <param name="chr_num" type="integer" value="22" label="Enter Chromosome Limit"/> 
    <!-- plink options -->
    <param name="noweb" argument="--noweb" type="boolean" truevalue="--noweb" falsevalue="" checked="false"                            
                    label="Noweb has no effect since no web check is implemented yet. " /> 
    <param name="chr" argument="--chr" type="boolean" truevalue="--chr" falsevalue="" checked="false"                            
                    label="All variants not on this given chromosome(s)" /> 
    <param name="makebed" argument="--make-bed" type="boolean" truevalue="--make-bed" falsevalue="" checked="false"                            
                    label="Create a new binary fileset." /> 
  </inputs>
        
  <outputs>
  	<collection type="list:list" label="Plink Chromosome(s) Collection List of List" name="output_plink_list_of_list">
        <discover_datasets pattern="input_file_chr(?P&lt;identifier_0&gt;.+)\.(?P&lt;identifier_1&gt;.+)" directory="output"/>
    </collection>
   </outputs> 
        
  <tests>
    <test>
      <param name="input_bed_file" value="test.bed" />
      <param name="input_bim_file" value="test.bim" />
      <param name="input_fam_file" value="test.fam" />      
      <output_collection name="pcoa" type="list:list">
        <element name="1">  
          <element name="bed" />
          <element name="bim" />
          <element name="fam" />
          <element name="log" />                            
        </element> 
      </output_collection>                           
    </test>
  </tests>
  <help><![CDATA[

  **What it does**

  PLINK v1.90b4 64-bit (20 Mar 2017)             www.cog-genomics.org/plink/1.9/
(C) 2005-2017 Shaun Purcell, Christopher Chang   GNU General Public License v3

  plink [input flag(s)...] {command flag(s)...} {other flag(s)...}
  plink --help {flag name(s)...}

Commands include --make-bed, --recode, --flip-scan, --merge-list,
--write-snplist, --list-duplicate-vars, --freqx, --missing, --test-mishap,
--hardy, --mendel, --ibc, --impute-sex, --indep-pairphase, --r2, --show-tags,
--blocks, --distance, --genome, --homozyg, --make-rel, --make-grm-gz,
--rel-cutoff, --cluster, --pca, --neighbour, --ibs-test, --regress-distance,
--model, --bd, --gxe, --logistic, --dosage, --lasso, --test-missing,
--make-perm-pheno, --tdt, --qfam, --annotate, --clump, --gene-report,
--meta-analysis, --epistasis, --fast-epistasis, and --score.

'plink --help | more' describes all functions (warning: long)

  ]]></help>
</tool>