Mercurial > repos > erasmus-medical-center > dr_disco

annotate dr-disco_classify.xml @ 10:f2c70d589596 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 3b03a60c8a46cc23f6fbbb9e32111b39c6044fad
author erasmus-medical-center
date Thu, 02 Nov 2017 05:17:31 -0400
parents 922b52cf9b35
children 3743fd602fa9
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1 <tool id="dr_disco_classify" name="Dr. Disco (classify)" version="@TOOL_VERSION@">
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2 <description>Classifies detected break-points in RNA-seq based on corresponding statistics and blacklists</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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8 <expand macro="requirements"/>
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9 <expand macro="version_command"/>
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11 <command detect_errors="exit_code"><![CDATA[
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12 dr-disco
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13 classify
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15 ${only_valid}
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17 #if $blacklist_regions:
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18 --blacklist-regions '${blacklist_regions}'
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19 #end if
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21 #if $blacklist_junctions:
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22 --blacklist-junctions '${blacklist_junctions}'
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23 #end if
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25 --min-chim-overhang '${min_chim_overhang}'
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27 '${dr_disco_detect_output}'
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28 '${dr_disco_classify_output}'
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29 ]]></command>
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31 <inputs>
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32 <param name="dr_disco_detect_output" type="data" format="tabular" label="Output of Dr. Disco Detect" />
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33 <param name="only_valid" argument="--only-valid" truevalue="--only-valid" falsevalue="" type="boolean" />
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35 <param name="blacklist_regions" argument="--blacklist-regions" type="data" format="bed" optional="True" label="Blacklist Regions" help="List of regions known to be false positives (https://github.com/yhoogstrate/dr-disco/tree/master/share/)" />
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36 <param name="blacklist_junctions" argument="--blacklist-junctions" type="data" format="tabular" optional="True" label="Blacklist Junctions" help="List of junctions know to be false positives (https://github.com/yhoogstrate/dr-disco/tree/master/share/)" />
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38 <param name="min_chim_overhang" type="integer" min="-1" value="50" label="Minimum alignment length on each side of the junction." help="May need to be set to smaller values for read lengths smaller than 75bp." argument="--min-chim-overhang" />
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39 </inputs>
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41 <outputs>
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42 <data name="dr_disco_classify_output" format="tabular" label="${tool.name} on ${dr_disco_detect_output.name}" />
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43 </outputs>
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45 <tests>
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46 <test>
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47 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
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48 <param name="only_valid" value="" />
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50 <output name="dr_disco_classify_output" file="classify_test_16.test-01.out.dbed" ftype="tabular" />
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51 </test>
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53 <test>
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54 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
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55 <param name="only_valid" value="--only-valid" />
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57 <output name="dr_disco_classify_output" file="classify_test_16.test-02.out.dbed" />
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58 </test>
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60 <test>
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61 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
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62 <param name="only_valid" />
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63 <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" />
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65 <output name="dr_disco_classify_output" file="classify_test_16.test-03.out.dbed" ftype="tabular" />
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66 </test>
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68 <test>
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69 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
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70 <param name="only_valid" />
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71 <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" />
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73 <output name="dr_disco_classify_output" file="classify_test_16.test-04.out.dbed" />
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74 </test>
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76 <test>
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77 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
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78 <param name="only_valid" />
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79 <param name="blacklist_junctions" value="blacklist-junctions.hg38.txt" ftype="tabular" />
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80
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81 <output name="dr_disco_classify_output" file="classify_test_16.test-05.out.dbed" ftype="tabular" />
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82 </test>
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83 <test>
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84 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
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85 <param name="only_valid" />
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86 <param name="blacklist_junctions" value="blacklist-junctions.hg38.txt" ftype="tabular" />
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87
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88 <output name="dr_disco_classify_output" file="classify_test_16.test-06.out.dbed" />
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89 </test>
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90 <test>
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91 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
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92 <param name="only_valid" />
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93 <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" />
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94 <param name="blacklist_junctions" value="blacklist-junctions.hg38.txt" ftype="tabular" />
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95
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96 <output name="dr_disco_classify_output" file="classify_test_16.test-07.out.dbed" ftype="tabular" />
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97 </test>
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98 <test>
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99 <param name="dr_disco_detect_output" value="classify_test_16.in.dbed" ftype="tabular" />
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100 <param name="only_valid" />
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101 <param name="blacklist_regions" value="blacklist-regions.hg38.bed" ftype="bed" />
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102 <param name="blacklist_junctions" value="blacklist-junctions.hg38.txt" ftype="tabular" />
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103
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104 <output name="dr_disco_classify_output" file="classify_test_16.test-08.out.dbed" />
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105 </test>
10
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106
3
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107 </tests>
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108
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109 <help><![CDATA[
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110
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111 **What it does**
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112
10
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113 It filters fusion events that are likely to be true or false based on a variety of parameters provided in the input table.
3
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114
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115 **Attributions**
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116
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117 This work is part of Youri Hoogstrate's PhD thesis.
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118
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119 ]]></help>
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120
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121 <expand macro="citations"/>
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122 </tool>