Mercurial > repos > iuc > homer_scanmotifgenomewide
comparison homer_scanMotifGenomeWide.xml @ 0:db456c398880 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
| author | iuc |
|---|---|
| date | Mon, 13 Dec 2021 15:13:33 +0000 |
| parents | |
| children | 465be78e9b05 |
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| -1:000000000000 | 0:db456c398880 |
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| 1 <tool id="homer_scanMotifGenomeWide" name="scanMotifGenomeWide" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05" license="MIT"> | |
| 2 <description/> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="xrefs"/> | |
| 7 <expand macro="requirements"/> | |
| 8 <command detect_errors="exit_code"><![CDATA[ | |
| 9 scanMotifGenomeWide.pl | |
| 10 '$motif' | |
| 11 #if str( $genome.source ) == "installed": | |
| 12 '$genome.all_fasta_source.fields.path' | |
| 13 #elif str( $genome.source ) == "history": | |
| 14 '$genome.fasta' | |
| 15 #end if | |
| 16 $bed | |
| 17 $keepAll | |
| 18 $mask | |
| 19 $Fivep | |
| 20 $homer1 | |
| 21 > | |
| 22 #if $bed: | |
| 23 '${output_bed}' | |
| 24 #else | |
| 25 '${output_text}' | |
| 26 #end if | |
| 27 ]]></command> | |
| 28 <inputs> | |
| 29 <param name="motif" type="data" format="txt" label="Motif file"/> | |
| 30 <conditional name="genome"> | |
| 31 <param name="source" type="select" label="Will you select a reference genome from your history or use a installed genome?"> | |
| 32 <option value="installed">Installed</option> | |
| 33 <option value="history">From History</option> | |
| 34 </param> | |
| 35 <when value="installed"> | |
| 36 <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> | |
| 37 <options from_data_table="all_fasta"> | |
| 38 <filter type="sort_by" column="2"/> | |
| 39 <validator type="no_options" message="No references are available"/> | |
| 40 </options> | |
| 41 </param> | |
| 42 </when> | |
| 43 <when value="history"> | |
| 44 <param name="fasta" type="data" format="fasta" label="Select reference genome"/> | |
| 45 </when> | |
| 46 </conditional> | |
| 47 <param argument="-bed" type="boolean" truevalue="-bed" falsevalue="" checked="false" label="Output bed format"/> | |
| 48 <param argument="-keepAll" type="boolean" truevalue="-keepAll" falsevalue="" checked="false" label="Report all motifs even if overlap" | |
| 49 help="By default, HOMER will remove a motif that overlaps itself, useful for palindromes. To report all, specify this option."/> | |
| 50 <param argument="-mask" type="boolean" truevalue="-mask" falsevalue="" checked="false" | |
| 51 label="Do not look for motifs in RepeatMasked sequence (lower case sequence in FASTA files)"/> | |
| 52 <param argument="-5p" name="Fivep" type="boolean" truevalue="-5p" falsevalue="" checked="false" | |
| 53 label="Report motif positions based on the 5' end of the motif sequence"/> | |
| 54 <param argument="-homer1" type="boolean" truevalue="-homer1" falsevalue="" checked="false" | |
| 55 label="Use homer1 instead of homer2"/> | |
| 56 </inputs> | |
| 57 <outputs> | |
| 58 <data format="tabular" name="output_text" label="${tool.name} on ${on_string}"> | |
| 59 <filter>bed is False</filter> | |
| 60 </data> | |
| 61 <data format="bed" name="output_bed" label="${tool.name} on ${on_string}"> | |
| 62 <filter>bed is True</filter> | |
| 63 </data> | |
| 64 </outputs> | |
| 65 <tests> | |
| 66 <test expect_num_outputs="1"> | |
| 67 <param name="motif" value="motif_test1/homerResults/motif1.motif"/> | |
| 68 <conditional name="genome"> | |
| 69 <param name="source" value="installed"/> | |
| 70 <param name="all_fasta_source" value="phiX174"/> | |
| 71 </conditional> | |
| 72 <output name="output_text" file="scanMotif_res1.txt" ftype="tabular"/> | |
| 73 </test> | |
| 74 <test expect_num_outputs="1"> | |
| 75 <param name="motif" value="motif_test1/homerResults/motif1.motif"/> | |
| 76 <conditional name="genome"> | |
| 77 <param name="source" value="history"/> | |
| 78 <param name="fasta" value="phiX174.fasta"/> | |
| 79 </conditional> | |
| 80 <param name="bed" value="-bed"/> | |
| 81 <output name="output_bed" file="scanMotif_res1.bed" ftype="bed"/> | |
| 82 </test> | |
| 83 </tests> | |
| 84 <help><![CDATA[ | |
| 85 | |
| 86 .. class:: infomark | |
| 87 | |
| 88 This is a wrapper for scanMotifGenomeWide.pl from HOMER but not all options are included. | |
| 89 | |
| 90 The scanMotifGenomeWide.pl script will take a motif file (may contain multiple motifs) and look for instances across the genome. | |
| 91 | |
| 92 ]]></help> | |
| 93 <expand macro="citation"/> | |
| 94 </tool> |