annotate subtract.xml @ 5:0145969324c4 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author devteam
date Thu, 22 Jun 2017 18:53:03 -0400
parents ecb36112b056
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1
7bf44b9d7a8b Corrected version string.
devteam <devteam@galaxyproject.org>
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1 <tool id="gops_subtract_1" name="Subtract" version="1.0.0">
5
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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2 <description>the intervals of two datasets</description>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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3 <macros>
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4 <import>macros.xml</import>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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5 </macros>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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6 <expand macro="requirements" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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7 <code file="operation_filter.py"/>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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8 <command><![CDATA[
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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9 python '$__tool_directory__/gops_subtract.py'
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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10 '$input1'
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11 '$input2'
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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12 '$output'
0
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13
5
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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14 #if $input1.is_of_type('gff')
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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15 -1 1,4,5,7 --gff1
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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16 #else:
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17 -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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18 #end if
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19
5
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20 #if $input2.is_of_type('gff')
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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21 -2 1,4,5,7 --gff2
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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22 #else:
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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23 -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol}
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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24 #end if
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25
5
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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26 -m $min
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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27 $returntype
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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28 ]]></command>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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29 <inputs>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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30 <param name="input2" type="data" format="interval,gff" label="Subtract" help="Second dataset" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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31 <param name="input1" type="data" format="interval,gff" label="from" help="First dataset" />
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32 <param name="returntype" type="select" label="Return" help="of the first dataset (see figure below)">
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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33 <option value="">Intervals with no overlap</option>
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34 <option value="-p">Non-overlapping pieces of intervals</option>
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35 </param>
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36 <param name="min" type="integer" value="1" min="1" label="where minimal overlap is" help="(bp)" />
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37 </inputs>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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38 <outputs>
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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39 <data name="output" format_source="input1" metadata_source="input1"/>
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="input1" value="1.bed" />
0145969324c4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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44 <param name="input2" value="2.bed" />
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45 <param name="min" value="1" />
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46 <param name="returntype" value="" />
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47 <output name="output" file="gops-subtract.dat" />
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48 </test>
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49 <test>
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50 <param name="input1" value="1.bed" />
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51 <param name="input2" value="2_mod.bed" ftype="interval"/>
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52 <param name="min" value="1" />
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53 <param name="returntype" value="" />
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54 <output name="output" file="gops_subtract_diffCols.dat" />
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55 </test>
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56 <test>
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57 <param name="input1" value="gops_subtract_bigint.bed" />
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58 <param name="input2" value="2.bed" />
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59 <param name="min" value="1" />
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60 <param name="returntype" value="" />
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61 <output name="output" file="gops-subtract.dat" />
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62 </test>
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63 <test>
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64 <param name="input1" value="1.bed" />
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65 <param name="input2" value="2.bed" />
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66 <param name="min" value="10" />
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67 <param name="returntype" value="Non-overlapping pieces of intervals" />
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68 <output name="output" file="gops-subtract-p.dat" />
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69 </test>
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70 <!-- Subtract two GFF files. -->
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71 <test>
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72 <param name="input1" value="gops_subtract_in1.gff" />
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73 <param name="input2" value="gops_subtract_in2.gff" />
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74 <param name="min" value="1" />
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75 <param name="returntype" value="" />
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76 <output name="output" file="gops_subtract_out1.gff" />
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77 </test>
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78 <!-- Subtract BED file from GFF file. -->
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79 <test>
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80 <param name="input1" value="gops_subtract_in1.gff" />
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81 <param name="input2" value="gops_subtract_in2.bed" />
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82 <param name="min" value="1" />
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83 <param name="returntype" value="" />
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84 <output name="output" file="gops_subtract_out1.gff" />
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85 </test>
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86 </tests>
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87 <help><![CDATA[
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88 .. class:: infomark
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89
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90 **TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns.
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91
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92 @SCREENCASTS@
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93
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94 **Syntax**
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95
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96 - **Where overlap is at least** sets the minimum length (in base pairs) of overlap between elements of the two datasets.
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97 - **Intervals with no overlap** returns entire intervals from the first dataset that do not overlap the second dataset. The returned intervals are completely unchanged, and this option only filters out intervals that overlap with the second dataset.
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98 - **Non-overlapping pieces of intervals** returns intervals from the first dataset that have the intervals from the second dataset removed. Any overlapping base pairs are removed from the range of the interval. All fields besides start and end are guaranteed to remain unchanged.
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99
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100 -----
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101
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102 **Example**
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103
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104 Intervals with no overlap:
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105
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106 .. image:: gops_subtractOverlappingIntervals.gif
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107
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108 Non-overlapping pieces of intervals:
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109
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110 .. image:: gops_subtractOverlappingPieces.gif
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111 ]]></help>
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112 </tool>