annotate dr-disco_classify.xml @ 11:3743fd602fa9 draft default tip

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 183cebdfe3a34204fd8aa1c6dce6bf6514b94c2d
author erasmus-medical-center
date Fri, 03 Nov 2017 07:23:57 -0400
parents f2c70d589596
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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
11
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113 * Step 3 in dr-disco pipeline
3
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114
11
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115 This tools filters the detected junctions which are likely to be true or false based on a variety of parameters provided in the input table. This filtering is in particular based on variables derived from the shape of the alignment and the ratio of split and spanning reads.
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116
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117 **Attribution**
3
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118
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119 This work is part of Youri Hoogstrate's PhD thesis.
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120
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121 ]]></help>
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122
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123 <expand macro="citations"/>
11
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124 </tool>