Mercurial > repos > jjohnson > bcftools_plugin_counts

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sun, 26 Jun 2016 15:37:20 -0400
parents 17b407921818
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17b407921818 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@VERSION@.0">
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3 <description>plugin counts number of samples, SNPs, INDELs, MNPs and total sites</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">counts</token>
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6 <token name="@PLUGIN_ID@">counts</token>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements" />
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10 <expand macro="version_command" />
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11 <command detect_errors="aggressive"><![CDATA[
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12 @PREPARE_ENV@
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13 @PREPARE_INPUT_FILE@
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14 #set $section = $sec_restrict
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15 @PREPARE_TARGETS_FILE@
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16 bcftools plugin @EXECUTABLE@
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17
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18 ## VCF input section
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19 #set $section = $sec_restrict
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20 @INCLUDE@
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21 @EXCLUDE@
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22 @REGIONS@
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23 @TARGETS@
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24
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25 ## Primary Input/Outputs
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26 @INPUT_FILE@ | tee counts_file.txt
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27 && sed 's/^.* \([a-zA-Z]*\):[ ]*\([0-9]*\)$/\1 \2/' counts_file.txt | python $transform > "$output_file"
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28 ]]>
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29 </command>
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30 <configfiles>
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31 <configfile name="transform">
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32 import sys
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33 header = []
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34 value = []
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35 for line in sys.stdin:
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36 h,v = line.strip().split()
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37 header.append(h)
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38 value.append(v)
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39 print >> sys.stdout, '#%s\n' % '\t'.join(header)
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40 print >> sys.stdout, '%s\n' % '\t'.join(value)
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41 </configfile>
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42 </configfiles>
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43 <inputs>
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44 <expand macro="macro_input" />
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45 <section name="sec_restrict" expanded="false" title="Restrict to">
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46 <expand macro="macro_regions" />
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47 <expand macro="macro_targets" />
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48 <expand macro="macro_include" />
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49 <expand macro="macro_exclude" />
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50 </section>
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51 </inputs>
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52 <outputs>
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53 <data name="output_file" format="tabular"/>
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54 </outputs>
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55 <tests>
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56 <test>
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57 <param name="input_file" ftype="vcf" value="view.vcf" />
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58 <output name="output_file">
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59 <assert_contents>
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60 <has_text text="SNPs"/>
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61 <has_text text="11"/>
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62 </assert_contents>
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63 </output>
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64 </test>
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65 </tests>
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66 <help><![CDATA[
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67 =====================================
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68 bcftools @EXECUTABLE@ plugin
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69 =====================================
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70
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71 Counts number of samples, SNPs, INDELs, MNPs and total number of sites.
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72
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73 @REGIONS_HELP@
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74 @TARGETS_HELP@
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75 @EXPRESSIONS_HELP@
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76
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77
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78
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79 ]]></help>
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80 <expand macro="citations" />
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81 </tool>