Mercurial > repos > morinlab > sequenza

annotate create_seqz_file.xml @ 3:235c8e5dfece draft default tip

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author morinlab
date Sun, 29 Jan 2017 11:42:51 -0500
parents a8359c3073ba
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73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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1 <tool id="create_seqz_file" name="Create Seqz File" version="2.1.2">
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2 <description>
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3 extracts the common positions containing A and B allele frequencies
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="2.1.2">sequenza</requirement>
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7 <requirement type="package" version="5.4.1">pypy</requirement>
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8 <requirement type="set_environment" version="2.1.2">SEQUENZA_INSTALL_DIR</requirement>
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9 </requirements>
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10 <command><![CDATA[
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11
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12 ln -s $normal normal.bam;
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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13 ln -s $normal.metadata.bam_index normal.bam.bai;
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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14 ln -s $tumour tumour.bam;
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15 ln -s $tumour.metadata.bam_index tumour.bam.bai;
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16
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17
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18 #if $reference_source.reference_source_selector == "history":
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19 ln -s $reference_source.ref_file reference.fa;
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20 samtools faidx reference.fa;
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21 #elif $reference_source.reference_source_selector == "cached":
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22 ln -s ${reference_source.ref_file.fields.path} reference.fa;
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23 #end if
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24
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25 EXEC=python;
1
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26 if [ \$(which pypy)!="" ] ; then
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27 EXEC=pypy;
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28 fi ;
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29
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30 #if $interval
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31 #if $gzip.gzip_selector == "yes"
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32 echo 1 >> $bytes;
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33 #end if
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34 for int in \$( cat $interval ); do
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35 #end if
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36
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37 #if $interval and $order_file
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38 if [ "\$int" != "\$( cat $order_file | head -n1)" ] ; then
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39 skip=2;
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40 else
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41 skip=1;
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42 fi ;
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43 #end if
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44
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45 \$EXEC \$SEQUENZA_INSTALL_DIR/sequenza/exec/sequenza-utils.py bam2seqz
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46 -n normal.bam
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47 -t tumour.bam
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48 -gc $gc_file
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49 -F reference.fa
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50
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51 #if $interval
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52 -C \$int
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53 #end if
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54
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55 --hom $geno.hom
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56 --het $geno.het
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57 -q $qual.qlimit
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58 -f $qual.qformat
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59 -N $qual.depth
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60
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61 | \$EXEC \$SEQUENZA_INSTALL_DIR/sequenza/exec/sequenza-utils.py seqz-binning
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62 -s -
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63 -w $window
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64
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65 | awk '{ if (\$4 >= $min_depth && \$5 >= $min_depth) print \$_ }'
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66
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67 #if $gzip.gzip_selector == "yes":
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68 #if $order_file and $interval:
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69 | tail -n+\$skip | gzip >> $output_gzip;
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70 #else
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71 | gzip >> $output_gzip;
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72 #end if
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73
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74 #if $interval:
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75 echo \$(( \$( wc -c < $output_gzip ) + 1 )) >> $bytes;
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76 #end if
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77
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78 #else:
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79 >> $output;
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80 #end if
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81
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82 #if $interval
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83 done;
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84 #end if
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85
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86 ]]></command>
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87 <inputs>
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88 <conditional name="reference_source">
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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89 <param label="Choose the source for the reference files" name="reference_source_selector" type="select">
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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90 <option value="cached">Locally Cached</option>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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91 <option value="history">History</option>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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92 </param>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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93 <when value="cached">
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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94 <param label="Genome" name="ref_file" type="select">
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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95 <options from_data_table="fasta_indexes"/>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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96 </param>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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97 </when>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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98 <when value="history">
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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99 <param label="Genome" name="ref_file" type="data" format="fasta"/>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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100 </when>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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101 </conditional>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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102 <param name="normal" label="Normal Alignment File (BAM)" type="data" format="data"/>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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103 <param name="tumour" label="Tumour Alignment File (BAM)" type="data" format="data"/>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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104 <param label="GC Window File" name="gc_file" type="data" format="tabular"/>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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105 <param label="Bin Output by Window" name="window" type="integer" min="1" max="50" value="50"/>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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106 <param name="min_depth" label="Minimum coverage for variant to be used in model" type="integer" min="1" max="50" value="12"/>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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107 <conditional name="gzip">
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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108 <param label="Should the output be gzipped" name="gzip_selector" type="select">
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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109 <option value="yes" selected="true">Yes</option>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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110 <option value="no">No</option>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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111 </param>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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112 </conditional>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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113 <param name="interval" optional="true" label="Restrict Computation to a particular Interval" help="Must be present in the BAM"
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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114 type="data" format="txt"/>
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115 <param name="order_file" optional="true" label="Order File" help="Should be Present with Interval File" type="data" format="txt"/>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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116 <section name="geno" title="Genotyping Options" expanded="False">
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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117 <param name="hom" label="Threshold to Select Homozygous Positions" type="float" value="0.9" min="0" max="1"/>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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118 <param name="het" label="Threshold to Select Heterozygous Positions" type="float" value="0.25" min="0" max="1"/>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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119 </section>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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120 <section name="qual" title="Quality Threshold Options" expanded="False">
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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121 <param name="depth" label="Treshold to Filter Positions" help="The sum of read depth in both samples" value="20" type="integer"/>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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122 <param name="qlimit" label="Minimum Nucleotide Quality Score" value="20" type="integer"/>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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123 <param name="qformat" label="Quality Format" type="select">
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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124 <option value="sanger">Sanger</option>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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125 <option value="illumina">Illumina</option>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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126 </param>
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127 </section>
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128 </inputs>
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129 <outputs>
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130 <data format="tabular" name="output" label="Seqz File">
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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131 <filter>gzip['gzip_selector'] == "no"</filter>
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132 </data>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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133 <data format="txt" name="output_gzip" label="Gzipped Seqz File">
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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134 <filter>gzip['gzip_selector'] == "yes"</filter>
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135 </data>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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136 <data format="txt" name="bytes" label="Gzip Block Locations">
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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137 <filter>gzip['gzip_selector'] == "yes"</filter>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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138 </data>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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139 </outputs>
73338a1805e7 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/sequenza commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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140 </tool>