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annotate macros.xml @ 1:8d8de66233ea draft

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planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
author iuc
date Sun, 15 Jul 2018 09:19:48 -0400
parents a584f046e4a7
children 4ce3441c407c
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a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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1 <macros>
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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2 <xml name="requirements">
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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3 <requirements>
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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4 <requirement type="package" version="@VERSION@">varscan</requirement>
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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5 <requirement type="package" version="4.2.1">gawk</requirement>
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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6 <yield/>
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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7 </requirements>
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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8 </xml>
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9
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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10 <token name="@VERSION@">2.4.3</token>
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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11
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12 <xml name="stdio">
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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13 <stdio>
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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14 <regex match="Exception" source="both" level="fatal" description="Tool exception"/>
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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15 <regex match=".*" source="both" level="log" description="tool progress"/>
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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16 </stdio>
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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17 <version_command><![CDATA[varscan 2>&1 | head -n 1]]></version_command>
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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18 </xml>
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19
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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20 <xml name="citations">
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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21 <citations>
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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22 <citation type="doi">10.1101/gr.129684.111</citation>
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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23 </citations>
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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24 </xml>
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25
1
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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26 <xml name="input_pileups">
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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27 <conditional name="pileup">
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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28 <param name="pileup_select" type="select" label="How do you want to provide your pileup files?" help="">
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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29 <option value="separated">As separated normal and tumor files</option>
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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30 <option value="combined">Normal and Tumor combined in one file</option>
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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31 </param>
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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32 <when value="separated">
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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33 <param name="normal_pileup" format="pileup" type="data" label="Samtools pileup dataset for Normal" help=""/>
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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34 <param name="tumor_pileup" format="pileup" type="data" label="Samtools pileup dataset for Tumor" help=""/>
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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35 </when>
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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36 <when value="combined">
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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37 <param name="combined_pileup" format="pileup" type="data" label="Samtools pileup dataset which has combined Normal and Tumor samples" help=""/>
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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38 </when>
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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39 </conditional>
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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40 </xml>
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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42 <token name="@INPUT_PILEUPS@">
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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43 #if $pileup.pileup_select == 'separated'
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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44 '${pileup.normal_pileup}'
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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45 '${pileup.tumor_pileup}'
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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46 galaxy_out
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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47 #else:
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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48 '${pileup.combined_pileup}'
8d8de66233ea planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177
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49 galaxy_out
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50 --mpileup 1
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51 #end if
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52
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53 </token>
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54
0
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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55 <xml name="min_coverage">
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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56 <param argument="--min-coverage" name="min_coverage" type="integer" value="8" min="1" max="200"
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57 label="Minimum read depth" help="Minimum depth at a position to make a call"/>
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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58 </xml>
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59 <xml name="min_reads2">
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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60 <param argument="--min-reads2" name="min_reads2" type="integer" value="2" min="1" max="200"
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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61 label="Minimum supporting reads" help="Minimum supporting reads at a position to make a call"/>
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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62 </xml>
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63 <xml name="min_avg_qual">
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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64 <param argument="--min-avg-qual" name="min_avg_qual" type="integer" value="15" min="1" max="50"
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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65 label="Minimum base quality at a position to count a read"/>
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66 </xml>
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67 <xml name="min_var_freq" token_value="0.01">
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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68 <param argument="--min-var-freq" name="min_var_freq" type="float" value="@VALUE@" min="0" max="1"
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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69 label="Minimum variant allele frequency threshold"/>
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70 </xml>
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71 <xml name="min_freq_for_hom">
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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72 <param argument="--min-freq-for-hom" name="min_freq_for_hom" type="float" value="0.75" min="0" max="1"
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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73 label="Minimum frequency to call homozygote"/>
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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74 </xml>
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75 <xml name="p_value" token_label="p-value threshold for calling variants" token_value="0.01">
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76 <param argument="--p-value" name="p_value" type="float" value="@VALUE@" min="0.0" max="1.0"
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77 label="@LABEL@"/>
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78 </xml>
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79 <xml name="strand_filter">
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80 <param name="strand_filter" type="select" label="Ignore variants with >90% support on one strand">
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81 <option value="no" selected="True">no</option>
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82 <option value="yes">yes</option>
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83 </param>
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84 </xml>
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85
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86 </macros>