Mercurial > repos > iuc > homer_findmotifsgenome
changeset 1:3126da33847c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
| author | iuc |
|---|---|
| date | Sun, 26 Sep 2021 12:29:15 +0000 |
| parents | ec974e69e0b5 |
| children | a8f207b43f64 |
| files | homer_findMotifsGenome.xml macros.xml test-data/fake_phix_peaks.subset.bed |
| diffstat | 3 files changed, 77 insertions(+), 8 deletions(-) [+] |
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--- a/homer_findMotifsGenome.xml Sun Aug 08 11:02:42 2021 +0000 +++ b/homer_findMotifsGenome.xml Sun Sep 26 12:29:15 2021 +0000 @@ -58,6 +58,14 @@ #end if #end if #end if +#if str( $background.use ) != "none": + -bg '$background.bg' +#end if +#if str( $background.use ) == "withbg": + -keepOverlappingBg +#else if str( $background.use ) == "chopify": + -chopify +#end if -len '$len' -S $S -mis $mis @@ -109,13 +117,18 @@ #elif str( $advanced.homer12.version ) == "homer1": -depth '$advanced.homer12.depth' #end if -#if not $nomotif: - && cp '${output}'/homerResults.html outputHomer.html - && cp -r '${output}' '${html_homer_file.files_path}' -#end if -#if not $motif_options.noknown: - && cp '${output}'/knownResults.html outputKnown.html - && cp -r '${output}' '${html_file.files_path}' +#if str( $background.use ) == "none": + #if not $nomotif: + && cp '${output}'/homerResults.html outputHomer.html + && cp -r '${output}' '${html_homer_file.files_path}' + #end if + #if not $motif_options.noknown: + && cp '${output}'/knownResults.html outputKnown.html + && cp -r '${output}' '${html_file.files_path}' + #end if +#else + && cp '${output}'/homerResults.html outputHomer.html + && cp -r '${output}' '${html_homer_file.files_path}' #end if ]]></command> <inputs> @@ -150,6 +163,24 @@ <expand macro="mask_size"/> </when> </conditional> + <conditional name="background"> + <param name="use" type="select" label="Will you use a background model?" > + <option value="none" selected="true" >No background model</option> + <option value="model" >Background model with regions removed from target Peak file</option> + <option value="withbg" >Background model with regions not removed from target Peak file</option> + <option value="chopify" >Chop large background model regions to the average size of target Peak file regions</option> + </param> + <when value="none"></when> + <when value="model"> + <param argument="-bg" type="data" format="bed,encodepeak,tabular" label="Background Peak file"/> + </when> + <when value="withbg"> + <param argument="-bg" type="data" format="bed,encodepeak,tabular" label="Background Peak file"/> + </when> + <when value="chopify"> + <param argument="-bg" type="data" format="bed,encodepeak,tabular" label="Background Peak file" /> + </when> + </conditional> <param argument="-len" type="text" value="8,10,12" label="comma-separated motif lengths" help="values greater 12 may cause the program to run out of memory - in these cases decrease the number of sequences analyzed (-N), or try analyzing shorter sequence regions (i.e. -size 100)"> <validator type="regex" message="motif lengths must be comma-separated integers without space">^(\d+,)*(\d+)$</validator> </param> @@ -222,6 +253,7 @@ <outputs> <data format="html" name="html_file" from_work_dir="outputKnown.html" label="${tool.name} on ${on_string}: Known motifs"> <filter>motif_options['noknown'] is False</filter> + <filter>background['use'] == "none"</filter> </data> <data format="html" name="html_homer_file" from_work_dir="outputHomer.html" label="${tool.name} on ${on_string}: De novo motifs"> <filter>nomotif is False</filter> @@ -304,6 +336,41 @@ </assert_contents> </output> </test> + <!-- background tests --> + <test expect_num_outputs="1"> + <param name="input" value="fake_phix_peaks.bed"/> + <conditional name="genome"> + <param name="source" value="installed"/> + <param name="all_fasta_source" value="phiX174"/> + </conditional> + <conditional name="background"> + <param name="use" value="withbg" /> + <param name="bg" value="fake_phix_peaks.subset.bed" /> + </conditional> + <output name="html_homer_file"> + <assert_contents> + <has_text text="HOXB13/MA0901.2/Jaspar(0.948)"/> + <has_text text="Yeast"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input" value="fake_phix_peaks.bed"/> + <conditional name="genome"> + <param name="source" value="installed"/> + <param name="all_fasta_source" value="phiX174"/> + </conditional> + <conditional name="background"> + <param name="use" value="chopify" /> + <param name="bg" value="fake_phix_peaks.subset.bed" /> + </conditional> + <output name="html_homer_file"> + <assert_contents> + <has_text text="CCA"/> + <has_text text="YAP5"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[
--- a/macros.xml Sun Aug 08 11:02:42 2021 +0000 +++ b/macros.xml Sun Sep 26 12:29:15 2021 +0000 @@ -4,7 +4,7 @@ This is the HOMER version that introduced the preparsed structure expected by the current version. --> <token name="@IDX_VERSION@">4.11</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="xrefs"> <xrefs> <xref type="bio.tools">homer</xref>