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1 <?xml version="1.0"?>
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2 <tool name="suspenders" id="bg_suspenders" version="0.2.5.0">
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3 <description>merging of labeled alignments</description>
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4 <requirements>
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5 <requirement type="package" version="0.2.5">suspenders</requirement>
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6 <requirement type="package" version="1.2.1">matplotlib</requirement>
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7 <requirement type="package" version="0.7.7">pysam</requirement>
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1:" />
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11 <exit_code range=":-1" />
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12 <regex match="Error:" />
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13 <regex match="Exception:" />
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14 </stdio>
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15 <command>
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16 <![CDATA[
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17 #set $inputs = ""
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18 #for $counter, $input_bam in enumerate( $reference_source.input_bams ):
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19 ln -s "${input_bam.input_bam}" "${counter}.bam";
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20 ln -s "${input_bam.input_bam.metadata.bam_index}" "${counter}.bai";
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21 set $inputs += '%s ' % $counter
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22 #end for
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23
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24 pysuspenders
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25 $labels
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26 $union
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27 $quality
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28 $pileup
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29 $image
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30 $mate_all
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31 $union_all
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32 $random_filter
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33 #if $chart:
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34 -c $image
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35 #end if
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36 -p \${GALAXY_SLOTS:-4}
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37 $output
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38 $inputs
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39 ]]>
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40 </command>
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41 <inputs>
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42 <repeat name="input_bams" title="BAM files" min="2" help="sorted by read name">
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43 <param name="input_bam" type="data" format="bam" label="BAM file">
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1
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44 <!--validator type="unspecified_build" />
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45 <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /-->
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46 </param>
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47 </repeat>
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48
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49 <param name="labels" type="boolean" truevalue="--lapels" falsevalue="--normal-input"
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50 checked="True"
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51 label="Input has lapels tags" help="--lapels/--normal-input" />
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52
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53 <param name="union" type="boolean" truevalue="--union" falsevalue=""
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54 label="Merge the files using the union filter" help="--union"/>
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55
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56 <param name="quality" type="boolean" truevalue="--quality" falsevalue=""
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57 checked="True" label="Merge the files using the quality filter" help="--quality"/>
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58
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59 <param name="pileup" type="boolean" truevalue="--pileup" falsevalue=""
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60 label="merge the files using the quality filter, then the pileup height filter" help="--pileup"/>
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61
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62 <param name="chart" type="boolean" truevalue="True" falsevalue="False"
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63 label="save pileup chart to an image" help=""/>
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64
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65 <param name="mate_all" type="boolean" truevalue="--mate-all" falsevalue=""
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66 label="compare unmated segments to mated ones" help="--mate-all"/>
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67
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68 <param name="union_all" type="boolean" truevalue="--union-all" falsevalue=""
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69 label="Use union filter if other filters fail" help="always active for --union (--union-all)"/>
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70
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71 <param name="random_filter" type="boolean" truevalue="--random-filer" falsevalue=""
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72 label="Use random filter if other filters fail" help="default for --quality and --pileup (--random-filter)"/>
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73
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74 </inputs>
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75 <outputs>
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76 <data name="output" format="bam" label="${tool.name} on ${on_string}"/>
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77 <data name="image" format="png" label="${tool.name} on ${on_string}: Chart">
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78 <filter>chart is True</filter>
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1
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79 </data>
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0
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80 </outputs>
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81 <tests>
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82
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83 </tests>
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84 <help>
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85 <![CDATA[
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86
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87 **What it does**
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88
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89 Allows the merging of alignments that have been annotated using pylapels into a single alignment that picks the highest quality alignment.
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90
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91 https://pypi.python.org/pypi/suspenders/
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92
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93 ]]>
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94 </help>
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95 </tool>
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