Mercurial > repos > iuc > homer_scanmotifgenomewide

annotate homer_scanMotifGenomeWide.xml @ 2:f15794662a69 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 15:00:57 +0000
parents 465be78e9b05
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
465be78e9b05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 16a919905f336e34e237388c1921d0f4f8a368af
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1 <tool id="homer_scanMotifGenomeWide" name="scanMotifGenomeWide" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
0
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2 <description/>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="xrefs"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 scanMotifGenomeWide.pl
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10 '$motif'
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11 #if str( $genome.source ) == "installed":
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12 '$genome.all_fasta_source.fields.path'
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13 #elif str( $genome.source ) == "history":
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14 '$genome.fasta'
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15 #end if
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16 $bed
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17 $keepAll
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18 $mask
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19 $Fivep
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20 $homer1
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21 >
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22 #if $bed:
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23 '${output_bed}'
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24 #else
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25 '${output_text}'
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26 #end if
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27 ]]></command>
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28 <inputs>
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29 <param name="motif" type="data" format="txt" label="Motif file"/>
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30 <conditional name="genome">
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31 <param name="source" type="select" label="Will you select a reference genome from your history or use a installed genome?">
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32 <option value="installed">Installed</option>
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33 <option value="history">From History</option>
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34 </param>
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35 <when value="installed">
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36 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
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37 <options from_data_table="all_fasta">
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38 <filter type="sort_by" column="2"/>
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39 <validator type="no_options" message="No references are available"/>
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40 </options>
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41 </param>
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42 </when>
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43 <when value="history">
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44 <param name="fasta" type="data" format="fasta" label="Select reference genome"/>
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45 </when>
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46 </conditional>
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47 <param argument="-bed" type="boolean" truevalue="-bed" falsevalue="" checked="false" label="Output bed format"/>
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48 <param argument="-keepAll" type="boolean" truevalue="-keepAll" falsevalue="" checked="false" label="Report all motifs even if overlap"
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49 help="By default, HOMER will remove a motif that overlaps itself, useful for palindromes. To report all, specify this option."/>
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50 <param argument="-mask" type="boolean" truevalue="-mask" falsevalue="" checked="false"
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51 label="Do not look for motifs in RepeatMasked sequence (lower case sequence in FASTA files)"/>
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52 <param argument="-5p" name="Fivep" type="boolean" truevalue="-5p" falsevalue="" checked="false"
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53 label="Report motif positions based on the 5' end of the motif sequence"/>
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54 <param argument="-homer1" type="boolean" truevalue="-homer1" falsevalue="" checked="false"
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55 label="Use homer1 instead of homer2"/>
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56 </inputs>
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57 <outputs>
1
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58 <data format="tabular" name="output_text" label="motif occurrences from ${tool.name} on ${on_string}">
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59 <filter>bed is False</filter>
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60 </data>
1
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61 <data format="bed" name="output_bed" label="motif occurrences from ${tool.name} on ${on_string} as bed">
0
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62 <filter>bed is True</filter>
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63 </data>
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64 </outputs>
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65 <tests>
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66 <test expect_num_outputs="1">
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67 <param name="motif" value="motif_test1/homerResults/motif1.motif"/>
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68 <conditional name="genome">
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69 <param name="source" value="installed"/>
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70 <param name="all_fasta_source" value="phiX174"/>
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71 </conditional>
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72 <output name="output_text" file="scanMotif_res1.txt" ftype="tabular"/>
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73 </test>
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74 <test expect_num_outputs="1">
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75 <param name="motif" value="motif_test1/homerResults/motif1.motif"/>
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76 <conditional name="genome">
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77 <param name="source" value="history"/>
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78 <param name="fasta" value="phiX174.fasta"/>
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79 </conditional>
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80 <param name="bed" value="-bed"/>
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81 <output name="output_bed" file="scanMotif_res1.bed" ftype="bed"/>
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82 </test>
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83 </tests>
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84 <help><![CDATA[
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85
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86 .. class:: infomark
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87
db456c398880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
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88 This is a wrapper for scanMotifGenomeWide.pl from HOMER but not all options are included.
db456c398880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
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89
db456c398880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
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90 The scanMotifGenomeWide.pl script will take a motif file (may contain multiple motifs) and look for instances across the genome.
db456c398880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
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91
db456c398880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
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92 ]]></help>
db456c398880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
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93 <expand macro="citation"/>
db456c398880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
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94 </tool>