Mercurial > repos > iuc > homer_annotatepeaks

annotate homer_annotatePeaks.xml @ 4:dcd291aeb8a9 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e6639e130c5bf50f489dd09e38a1cbc712280fff
author iuc
date Fri, 07 Apr 2023 15:03:57 +0000
parents fa7c3a74acf2
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
fa7c3a74acf2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 16a919905f336e34e237388c1921d0f4f8a368af
iuc
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1 <tool id="homer_annotatePeaks" name="annotatePeaks" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
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2 <macros>
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3 <import>macros.xml</import>
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4 </macros>
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5 <expand macro="requirements"/>
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6 <command detect_errors="exit_code"><![CDATA[
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7 annotatePeaks.pl
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8 ## Peak file
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9 '$input'
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10 ## Genome
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11 #if $CpG.bool == "true":
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12 #if $CpG.genome.source == 'installed':
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13 '${CpG.genome.all_fasta_source.fields.path}'
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14 #else
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15 '${CpG.genome.fasta}'
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16 #end if
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17 -CpG
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18 #else
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19 none
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20 #end if
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21 #if $gtf_file:
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22 -gtf '$gtf_file'
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23 #end if
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24 #if $ann_file:
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25 -ann '$ann_file'
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26 #end if
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27 > '$output'
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28 ]]></command>
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29 <inputs>
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30 <param name="input" type="data" format="bed,encodepeak,tabular" label="Peak file"/>
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31 <!-- CpG -->
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32 <conditional name="CpG">
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33 <param name="bool" type="select" label="Do you want to compute CpG/GC content?">
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34 <option value="true">Yes</option>
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35 <option value="false">No</option>
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36 </param>
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37 <when value="true">
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38 <conditional name="genome">
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39 <param name="source" type="select" label="Will you select a reference genome from your history or use a installed genome?">
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40 <option value="installed">Installed</option>
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41 <option value="history">From History</option>
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42 </param>
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43 <when value="installed">
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44 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
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45 <options from_data_table="all_fasta">
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46 <filter type="sort_by" column="2"/>
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47 <validator type="no_options" message="No references are available"/>
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48 </options>
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49 </param>
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50 </when>
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51 <when value="history">
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52 <param name="fasta" type="data" format="fasta" label="Select reference genome"/>
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53 </when>
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54 </conditional>
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55 </when>
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56 <when value="false"/>
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57 </conditional>
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58 <param name="gtf_file" type="data" format="gtf,gff,gff3" optional="True" label="GTF file" help="Must be of datatype &quot;gtf&quot; or &quot;gff&quot; or &quot;gff3&quot;" argument="-gtf"/>
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59 <param name="ann_file" type="data" format="tabular" optional="True" label="Annotation data file for HOMER" help="This file can be generated from gtf with the tool 'Converts GTF to Annotations file for Homer" argument="-ann"/>
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60 </inputs>
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61 <outputs>
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62 <data format="tabular" name="output"/>
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63 </outputs>
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64 <tests>
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65 <test expect_num_outputs="1">
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66 <!-- first simple test with ann and gtf-->
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67 <param name="input" value="CTCF_peaks.bed" ftype="bed"/>
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68 <conditional name="CpG">
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69 <param name="bool" value="false"/>
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70 </conditional>
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71 <param name="ann_file" value="annotations_default_simplified.txt" ftype="tabular"/>
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72 <param name="gtf_file" value="small_simplified.gtf" ftype="gtf"/>
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73 <output name="output" file="CTCF_peaks_first.txt" ftype="tabular" compare="diff" lines_diff="2"/>
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74 </test>
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75 <test expect_num_outputs="1">
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76 <!-- second simple test with ann only-->
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77 <param name="input" value="CTCF_peaks.bed" ftype="bed"/>
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78 <conditional name="CpG">
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79 <param name="bool" value="false"/>
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80 </conditional>
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81 <param name="ann_file" value="annotations_default.txt" ftype="tabular"/>
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82 <output name="output" file="CTCF_peaks_second.txt" ftype="tabular" compare="diff" lines_diff="2"/>
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83 </test>
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84 <test expect_num_outputs="1">
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85 <!-- third simple test with gtf only-->
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86 <param name="input" value="CTCF_peaks.bed" ftype="bed"/>
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87 <conditional name="CpG">
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88 <param name="bool" value="false"/>
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89 </conditional>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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90 <param name="gtf_file" value="small_simplified.gtf" ftype="gtf"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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91 <output name="output" file="CTCF_peaks_third.txt" ftype="tabular" compare="diff" lines_diff="2"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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92 </test>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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93 <test expect_num_outputs="1">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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94 <!--test with CpG-->
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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95 <param name="input" value="fake_phix_peaks.bed"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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96 <conditional name="CpG">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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97 <param name="bool" value="true"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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98 <conditional name="genome">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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99 <param name="source" value="history"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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100 <param name="fasta" value="phiX174.fasta"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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101 </conditional>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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102 </conditional>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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103 <output name="output" file="phiXcpg.txt" ftype="tabular" compare="diff" lines_diff="2"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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104 </test>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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105 <test expect_num_outputs="1">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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106 <!--test with CpG from table-->
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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107 <param name="input" value="fake_phix_peaks.bed"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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108 <conditional name="CpG">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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109 <param name="bool" value="true"/>
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110 <conditional name="genome">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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111 <param name="source" value="installed"/>
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112 <param name="all_fasta_source" value="phiX174"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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113 </conditional>
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114 </conditional>
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115 <output name="output" file="phiXcpg.txt" ftype="tabular" compare="diff" lines_diff="2"/>
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116 </test>
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117 <test expect_num_outputs="1">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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118 <!--test with nothing-->
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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119 <param name="input" value="fake_phix_peaks.bed"/>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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120 <conditional name="CpG">
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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121 <param name="bool" value="false"/>
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122 </conditional>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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123 <output name="output" file="phiX_nothing.txt" ftype="tabular" compare="diff" lines_diff="2"/>
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124 </test>
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125 </tests>
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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126 <help><![CDATA[
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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127 This wrapper allow to annotate peaks with simple annotations with annotatePeaks.pl from HOMER.
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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128 The annotation file and the GTF file may seem redundant but:
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129 - the use of gtf file only misses the UTR annotations and does not allow to set the desired offsets for TSS and TTS.
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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130 - the use of annotation file only misses the distance to tss and the correspondance between id and classical gene name.
adab852c8216 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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131 ]]></help>
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132 <expand macro="citation"/>
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133 </tool>