Mercurial > repos > dave > all_tests_pass

annotate qorts_qc.xml @ 6:cdf1d1b10523 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qorts commit 1f232ed80ea6ef2192647e293040a22c9733b260-dirty
author dave
date Fri, 13 Nov 2015 15:44:38 -0500
parents d9a61a9529e6
children
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68e581bd3a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qorts commit 1f232ed80ea6ef2192647e293040a22c9733b260-dirty
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1 <tool name="QoRTs" id="qorts_qc" version="1.0.0">
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2 <macros>
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3 <import>qorts_macros.xml</import>
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4 </macros>
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5 <expand macro="requirements" />
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6 <description>quality control RNA-Seq reads</description>
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7 <command><![CDATA[
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8 @QORTS_INVOCATION@ QC --noGzipOutput --generatePlots
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9 #if 'makeWiggles' in str( $functions ).split( ',' ):
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10 --chromSizes "${chromInfo}"
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11 #end if
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12 --minMAPQ $min_mapq
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13 --runFunctions $functions
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14 "${input_dataset}" "${gff_file}" .
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15 > "${stdio}" 2>&1
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16 ]]>
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17 </command>
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18 <stdio>
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19 <exit_code range="1:" level="fatal" description="SNAFU" />
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20 </stdio>
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21 <inputs>
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22 <param format="sam,bam" label="SAM or BAM file to QC" name="input_dataset" type="data" />
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23 <param format="gff" label="GFF file" name="gff_file" type="data" />
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24 <param name="min_mapq" label="Filter out reads with less than the given MAPQ" type="integer" value="255" />
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25 <param name="functions" type="select" multiple="True" display="checkboxes" label="Functions to execute" help="--runFunctions">
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26 <option selected="True" value="NVC">Nucleotide-vs-Cycle counts</option>
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27 <option selected="True" value="GCDistribution">Calculate GC content distribution</option>
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28 <option selected="True" value="GeneCalcs">Find gene assignment and gene body calculations</option>
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29 <option selected="True" value="QualityScoreDistribution">Calculate quality scores by cycle</option>
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30 <option selected="True" value="writeJunctionSeqCounts">Write counts file designed for use with JunctionSeq</option>
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31 <option selected="True" value="writeKnownSplices">Write known splice junction counts</option>
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32 <option selected="True" value="writeNovelSplices">Write novel splice junction counts</option>
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33 <option selected="True" value="writeClippedNVC">Write NVC file containing clipped sequences</option>
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34 <option selected="True" value="CigarOpDistribution">Cigar operation rates by cycle and cigar operation length rates</option>
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35 <option selected="True" value="InsertSize">Insert size distribution</option>
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36 <option selected="True" value="chromCounts">Calculate chromosome counts</option>
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37 <option selected="True" value="writeGenewiseGeneBody">Write file containing gene-body distributions for each gene</option>
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38 <option selected="True" value="JunctionCalcs">Find splice junctions</option>
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39 <option selected="True" value="writeGeneCounts">Write extended gene-level read/read-pair counts file</option>
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40 <option selected="True" value="writeDESeq">Write gene-level read/read-pair counts for use with DESeq, EdgeR, etc</option>
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41 <option selected="True" value="writeDEXSeq">Write exon-level read/read-pair counts file, designed for use with DEXSeq</option>
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42 <option selected="True" value="writeGeneBody">Write gene-body distribution file</option>
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43 <option selected="True" value="StrandCheck">Check the strandedness of the data</option>
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44 <option value="annotatedSpliceExonCounts">Write counts for exons, known-splice-junctions, and genes</option>
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45 <option value="FPKM">Write FPKM values</option>
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46 <option value="makeJunctionBed,writeJunctionSeqCounts,writeSpliceExon,JunctionCalcs">Write splice-junction count "bed" files</option>
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47 <option value="makeWiggles">Write "wiggle" coverage files with 100-bp window size</option>
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48 <option value="makeAllBrowserTracks">Write both the "wiggle" and the splice-junction bed files</option>
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49 </param>
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50 </inputs>
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51 <outputs>
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52 <data name="stdio" format="txt" label="${tool.name} on ${on_string}: Tool execution output" />
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53 <data name="tool_log" format="txt" from_work_dir="QC.log" label="${tool.name} on ${on_string}: Log file" />
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54 <data name="summary" format="tabular" from_work_dir="QC.summary.txt" label="${tool.name} on ${on_string}: Summary data" />
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55 <data name="multiplot" format="png" from_work_dir="QC.multiPlot.png" label="${tool.name} on ${on_string}: Summary plots" />
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56 <data name="nvc_mc_r1" format="tabular" from_work_dir="QC.NVC.minus.clipping.R1.txt" label="${tool.name} on ${on_string}: NVC minus clipping R1">
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57 <filter>('NVC' in functions)</filter>
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58 </data>
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59 <data name="nvc_mc_r2" format="tabular" from_work_dir="QC.NVC.minus.clipping.R1.txt" label="${tool.name} on ${on_string}: NVC minus clipping R2">
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60 <filter>('NVC' in functions)</filter>
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61 </data>
5
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62 <data name="nvc_raw_r1" format="tabular" from_work_dir="QC.NVC.minus.clipping.R1.txt" label="${tool.name} on ${on_string}: NVC raw R 1">
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63 <filter>('NVC' in functions or 'writeClippedNVC' in functions)</filter>
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64 </data>
6
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65 <data name="nvc_raw_r2" format="tabular" from_work_dir="QC.NVC.minus.clipping.R1.txt" label="${tool.name} on ${on_string}: NVC raw R 2">
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66 <filter>('NVC' in functions or 'writeClippedNVC' in functions)</filter>
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67 </data>
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68 <data name="gc_bypair" format="tabular" from_work_dir="QC.gc.byPair.txt" label="${tool.name} on ${on_string}: GC distribution by pair">
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69 <filter>('GCDistribution' in functions)</filter>
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70 </data>
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71 <data name="gc_byread" format="tabular" from_work_dir="QC.gc.byRead.txt" label="${tool.name} on ${on_string}: GC distribution by read">
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72 <filter>('GCDistribution' in functions)</filter>
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73 </data>
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74 <data name="gc_vsbasect" format="tabular" from_work_dir="QC.gc.byRead.vsBaseCt.txt" label="${tool.name} on ${on_string}: GC vs. base ct">
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75 <filter>('GCDistribution' in functions)</filter>
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76 </data>
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77 <data name="gc_r1" format="tabular" from_work_dir="QC.gc.R1.txt" label="${tool.name} on ${on_string}: R1 GC distribution">
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78 <filter>('GCDistribution' in functions)</filter>
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79 </data>
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80 <data name="gc_r2" format="tabular" from_work_dir="QC.gc.R2.txt" label="${tool.name} on ${on_string}: R2 GC distribution">
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81 <filter>('GCDistribution' in functions)</filter>
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82 </data>
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83 <data name="quals_r1" format="tabular" from_work_dir="QC.quals.r1.txt" label="${tool.name} on ${on_string}: R1 quality score distribution">
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84 <filter>('QualityScoreDistribution' in functions)</filter>
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85 </data>
68e581bd3a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qorts commit 1f232ed80ea6ef2192647e293040a22c9733b260-dirty
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86 <data name="quals_r2" format="tabular" from_work_dir="QC.quals.r2.txt" label="${tool.name} on ${on_string}: R2 quality score distribution">
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87 <filter>('QualityScoreDistribution' in functions)</filter>
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88 </data>
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89 <data name="splice_exon_junctionseq" format="tabular" from_work_dir="QC.quals.r2.txt" label="${tool.name} on ${on_string}: Splice junctions, exon counts (for JunctionSeq)">
68e581bd3a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qorts commit 1f232ed80ea6ef2192647e293040a22c9733b260-dirty
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90 <filter>('writeJunctionSeqCounts' in functions or 'makeJunctionBed,writeJunctionSeqCounts,writeSpliceExon,JunctionCalcs' in functions)</filter>
68e581bd3a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qorts commit 1f232ed80ea6ef2192647e293040a22c9733b260-dirty
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91 </data>
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92 <data name="known_splice_count" format="tabular" from_work_dir="QC.spliceJunctionCounts.knownSplices.txt" label="${tool.name} on ${on_string}: Known splice junction counts">
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93 <filter>('writeKnownSplices' in functions)</filter>
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94 </data>
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95 <data name="novel_splice_count" format="tabular" from_work_dir="QC.spliceJunctionCounts.novelSplices.txt" label="${tool.name} on ${on_string}: Novel splice junction counts">
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96 <filter>('writeNovelSplices' in functions)</filter>
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97 </data>
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98 <data name="exons_splice_junctions" format="txt" from_work_dir="QC.annoSpliceJunctionAndExonCounts.txt" label="${tool.name} on ${on_string}: Exons, known splice junctions, genes">
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99 <filter>('annotatedSpliceExonCounts' in functions)</filter>
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100 </data>
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101 <data name="nvc_tail_clip_r1" format="tabular" from_work_dir="QC.NVC.tail.clip.R1.txt" label="${tool.name} on ${on_string}: QC.NVC.tail.clip.R1.txt">
68e581bd3a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qorts commit 1f232ed80ea6ef2192647e293040a22c9733b260-dirty
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102 <filter>('writeClippedNVC' in functions)</filter>
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103 </data>
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104 <data name="nvc_tail_clip_r2" format="tabular" from_work_dir="QC.NVC.tail.clip.R2.txt" label="${tool.name} on ${on_string}: QC.NVC.tail.clip.R2.txt">
68e581bd3a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qorts commit 1f232ed80ea6ef2192647e293040a22c9733b260-dirty
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105 <filter>('writeClippedNVC' in functions)</filter>
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106 </data>
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107 <data name="nvc_lead_clip_r1" format="tabular" from_work_dir="QC.NVC.lead.clip.R1.txt" label="${tool.name} on ${on_string}: QC.NVC.lead.clip.R1.txt">
68e581bd3a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qorts commit 1f232ed80ea6ef2192647e293040a22c9733b260-dirty
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108 <filter>('writeClippedNVC' in functions)</filter>
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109 </data>
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110 <data name="nvc_lead_clip_r2" format="tabular" from_work_dir="QC.NVC.lead.clip.R2.txt" label="${tool.name} on ${on_string}: QC.NVC.lead.clip.R2.txt">
68e581bd3a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qorts commit 1f232ed80ea6ef2192647e293040a22c9733b260-dirty
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111 <filter>('writeClippedNVC' in functions)</filter>
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112 </data>
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113 <data name="nvc_raw_r1" format="tabular" from_work_dir="QC.NVC.raw.R1.txt" label="${tool.name} on ${on_string}: QC.NVC.raw.R1.txt">
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114 <filter>('writeClippedNVC' in functions)</filter>
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115 </data>
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116 <data name="nvc_raw_r2" format="tabular" from_work_dir="QC.NVC.raw.R2.txt " label="${tool.name} on ${on_string}: QC.NVC.raw.R2.txt ">
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117 <filter>('writeClippedNVC' in functions)</filter>
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118 </data>
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119 <data name="cigar_rc_r1" format="tabular" from_work_dir="QC.cigarOpDistribution.byReadCycle.R1.txt" label="${tool.name} on ${on_string}: QC.cigarOpDistribution.byReadCycle.R1.txt">
68e581bd3a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qorts commit 1f232ed80ea6ef2192647e293040a22c9733b260-dirty
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120 <filter>('CigarOpDistribution' in functions)</filter>
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121 </data>
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122 <data name="cigar_rc_r2" format="tabular" from_work_dir="QC.cigarOpDistribution.byReadCycle.R2.txt" label="${tool.name} on ${on_string}: QC.cigarOpDistribution.byReadCycle.R2.txt">
68e581bd3a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qorts commit 1f232ed80ea6ef2192647e293040a22c9733b260-dirty
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123 <filter>('CigarOpDistribution' in functions)</filter>
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124 </data>
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125 <data name="cigar_op_r1" format="tabular" from_work_dir="QC.cigarOpLengths.byOp.R2.txt" label="${tool.name} on ${on_string}: QC.cigarOpLengths.byOp.R2.txt">
68e581bd3a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qorts commit 1f232ed80ea6ef2192647e293040a22c9733b260-dirty
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126 <filter>('CigarOpDistribution' in functions)</filter>
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127 </data>
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128 <data name="cigar_op_r2" format="tabular" from_work_dir="QC.cigarOpLengths.byOp.R1.txt" label="${tool.name} on ${on_string}: QC.cigarOpLengths.byOp.R1.txt">
68e581bd3a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qorts commit 1f232ed80ea6ef2192647e293040a22c9733b260-dirty
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129 <filter>('CigarOpDistribution' in functions)</filter>
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130 </data>
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131 <data name="is_debug_dropped" format="tabular" from_work_dir="QC.insert.size.debug.dropped.txt" label="${tool.name} on ${on_string}: QC.insert.size.debug.dropped.txt">
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132 <filter>('InsertSize' in functions)</filter>
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133 </data>
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134 <data name="is_debug" format="tabular" from_work_dir="QC.insert.size.debug.txt" label="${tool.name} on ${on_string}: QC.insert.size.debug.txt">
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135 <filter>('InsertSize' in functions)</filter>
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136 </data>
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137 <data name="insert_size" format="tabular" from_work_dir="QC.insert.size.txt" label="${tool.name} on ${on_string}: QC.insert.size.txt">
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138 <filter>('InsertSize' in functions)</filter>
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139 </data>
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140 <data name="chrom_count" format="tabular" from_work_dir="QC.chromCount.txt" label="${tool.name} on ${on_string}: QC.chromCount.txt">
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141 <filter>('chromCounts' in functions)</filter>
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142 </data>
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143 <data name="gene_count" format="tabular" from_work_dir="QC.geneCounts.txt" label="${tool.name} on ${on_string}: Gene counts">
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144 <filter>('writeGeneCounts' in functions)</filter>
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145 </data>
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146 <data name="gene_count_deseq" format="tabular" from_work_dir="QC.geneCounts.formatted.for.DESeq.txt" label="${tool.name} on ${on_string}: Gene Counts (DESeq formatted)">
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147 <filter>('writeDESeq' in functions)</filter>
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148 </data>
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149 <data name="exon_count_desseq" format="tabular" from_work_dir="QC.exonCounts.formatted.for.DEXSeq.txt" label="${tool.name} on ${on_string}: Exon Counts (DEXSeq formatted)">
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150 <filter>('writeDEXSeq' in functions)</filter>
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151 </data>
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152 <data name="gbc_expression" format="tabular" from_work_dir="QC.geneBodyCoverage.by.expression.level.txt" label="${tool.name} on ${on_string}: QC.geneBodyCoverage.by.expression.level.txt">
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153 <filter>('writeGeneBody' in functions)</filter>
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154 </data>
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155 <data name="gbc_debug" format="tabular" from_work_dir="QC.geneBodyCoverage.DEBUG.intervals.txt.gz" label="${tool.name} on ${on_string}: QC.geneBodyCoverage.DEBUG.intervals.txt.gz">
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156 <filter>('writeGeneBody' in functions)</filter>
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157 </data>
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158 <data name="known_splice_bed" format="bed" from_work_dir="QC.junctionBed.known.bed.gz" label="${tool.name} on ${on_string}: Known splice junctions">
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159 <filter>('makeJunctionBed,writeJunctionSeqCounts,writeSpliceExon,JunctionCalcs' in functions or 'makeAllBrowserTracks' in functions)</filter>
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160 </data>
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161 <data name="" format="wig" from_work_dir="QC.wiggle.unstranded.wig" label="${tool.name} on ${on_string}: QC.wiggle.unstranded.wig">
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162 <filter>('makeWiggles' in functions or 'makeAllBrowserTracks' in functions)</filter>
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163 </data>
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164 </outputs>
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165 </tool>