Mercurial > repos > bgruening > hicexplorer_chicexportdata
comparison chicExportData.xml @ 1:163fd744e235 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 8586409c5f329eaf75902eedc3d29a6e82560788
| author | iuc |
|---|---|
| date | Mon, 01 Jul 2024 20:03:39 +0000 |
| parents | 23b8d6b8960c |
| children |
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| 0:23b8d6b8960c | 1:163fd744e235 |
|---|---|
| 1 <tool id="hicexplorer_chicexportdata" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> | 1 <tool id="hicexplorer_chicexportdata" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
| 2 <description>exports data of hdf to txt based files</description> | 2 <description>exports data of hdf to txt based files</description> |
| 3 <macros> | 3 <macros> |
| 4 <token name="@BINARY@">chicExportData</token> | 4 <token name="@BINARY@">chicExportData</token> |
| 5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
| 6 </macros> | 6 </macros> |
| 7 <expand macro="requirements" /> | 7 <expand macro="requirements" /> |
| 8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
| 9 #import re | 9 #import re |
| 10 mkdir exportFolder && | 10 mkdir exportFolder && |
| 11 @BINARY@ | 11 @BINARY@ |
| 12 --file '$file' | 12 --file '$file' |
| 13 | 13 |
| 14 #if $fileType_conditional.fileType_selector == 'interaction': | 14 #if $fileType_conditional.fileType_selector == 'interaction': |
| 15 #if $fileType_conditional.txtBigwig_conditional.txtBigwig_selector == 'txt': | 15 #if $fileType_conditional.txtBigwig_conditional.txtBigwig_selector == 'txt': |
| 31 --outputMode $outputMode_conditional.outputMode_selector | 31 --outputMode $outputMode_conditional.outputMode_selector |
| 32 #if $outputMode_conditional.outputMode_selector == 'geneName': | 32 #if $outputMode_conditional.outputMode_selector == 'geneName': |
| 33 --outputModeName $outputMode_conditional.outputModeName | 33 --outputModeName $outputMode_conditional.outputModeName |
| 34 #end if | 34 #end if |
| 35 --decimalPlaces $decimalPlaces | 35 --decimalPlaces $decimalPlaces |
| 36 | |
| 37 --outFileName exportFolder/export.tar.gz | 36 --outFileName exportFolder/export.tar.gz |
| 38 --threads @THREADS@ | 37 --threads @THREADS@ |
| 39 | 38 |
| 40 ]]> </command> | 39 ]]></command> |
| 41 <inputs> | 40 <inputs> |
| 42 | |
| 43 <param name="file" type="data" format="h5" label="" /> | 41 <param name="file" type="data" format="h5" label="" /> |
| 44 <conditional name="fileType_conditional"> | 42 <conditional name="fileType_conditional"> |
| 45 | 43 |
| 46 <param name="fileType_selector" type="select" label="Combination mode for the plots"> | 44 <param name="fileType_selector" type="select" label="Combination mode for the plots"> |
| 47 <option value="interaction" selected="True">Interaction file (from chicViewpoint)</option> | 45 <option value="interaction" selected="True">Interaction file (from chicViewpoint)</option> |
| 57 <option value="bigwig">BigWig</option> | 55 <option value="bigwig">BigWig</option> |
| 58 </param> | 56 </param> |
| 59 <when value="txt" > | 57 <when value="txt" > |
| 60 </when> | 58 </when> |
| 61 <when value="bigwig" > | 59 <when value="bigwig" > |
| 62 <param name="rangeUpstream" type="integer" value="500000" label="Upstream range" help="Defines the region upstream of a reference point which should be considered in the analysis." /> | 60 <param name="rangeUpstream" type="integer" value="500000" label="Upstream range" |
| 63 <param name="rangeDownstream" type="integer" value="500000" label="Downstream range" help="Defines the region upstream of a reference point which should be considered in the analysis." /> | 61 help="Defines the region upstream of a reference point which should be considered in the analysis." /> |
| 62 <param name="rangeDownstream" type="integer" value="500000" label="Downstream range" | |
| 63 help="Defines the region upstream of a reference point which should be considered in the analysis." /> | |
| 64 <param name="column_selector" type="select" label="Datatrack output type"> | 64 <param name="column_selector" type="select" label="Datatrack output type"> |
| 65 <option value="relative-interactions" selected="True">relative interactions</option> | 65 <option value="relative-interactions" selected="True">relative interactions</option> |
| 66 <option value="p-value">p-value</option> | 66 <option value="p-value">p-value</option> |
| 67 <option value="x-fold" >x-fold</option> | 67 <option value="x-fold" >x-fold</option> |
| 68 <option value="raw" >raw</option> | 68 <option value="raw" >raw</option> |
| 69 </param> | 69 </param> |
| 70 <param name="backgroundModelFile" type="data" format="tabular" label="Background model" help="The background file computed by chicViewpointBackgroundModel" /> | 70 <param name="backgroundModelFile" type="data" format="tabular" label="Background model" |
| 71 <param name="chromosomeSize" type="data" format="tabular" label="Chromosome size" help="Chromosome size as tabular file. One chromosome per line" /> | 71 help="The background file computed by chicViewpointBackgroundModel" /> |
| 72 <param name="chromosomeSize" type="data" format="tabular" label="Chromosome size" | |
| 73 help="Chromosome size as tabular file. One chromosome per line" /> | |
| 72 </when> | 74 </when> |
| 73 </conditional> | 75 </conditional> |
| 74 </when> | 76 </when> |
| 75 <when value="aggregate" > | 77 <when value="aggregate" > |
| 76 </when> | 78 </when> |
| 134 <conditional name="outputMode_conditional"> | 136 <conditional name="outputMode_conditional"> |
| 135 <param name="outputMode_selector" value="geneName" /> | 137 <param name="outputMode_selector" value="geneName" /> |
| 136 <param name="outputModeName" value="Eya1" /> | 138 <param name="outputModeName" value="Eya1" /> |
| 137 </conditional> | 139 </conditional> |
| 138 <output_collection name="oneGeneCollectionBigwig" type="list" count="4"> | 140 <output_collection name="oneGeneCollectionBigwig" type="list" count="4"> |
| 141 <element name="FL-E13-5_chr1_genes_Eya1.bigwig" file="cHi-C/chicExportData/oneGene/FL-E13-5_chr1_genes_Eya1.bigwig" ftype="bigwig" compare="sim_size" /> | |
| 142 <element name="MB-E10-5_chr1_genes_Eya1.bigwig" file="cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1.bigwig" ftype="bigwig" compare="sim_size" /> | |
| 139 <element name="background_FL-E13-5_chr1_genes_Eya1_interactions.bigwig" file="cHi-C/chicExportData/oneGene/background_FL-E13-5_chr1_genes_Eya1_interactions.bigwig" ftype="bigwig" compare="sim_size" /> | 143 <element name="background_FL-E13-5_chr1_genes_Eya1_interactions.bigwig" file="cHi-C/chicExportData/oneGene/background_FL-E13-5_chr1_genes_Eya1_interactions.bigwig" ftype="bigwig" compare="sim_size" /> |
| 140 <element name="background_MB-E10-5_chr1_genes_Eya1_interactions.bigwig" file="cHi-C/chicExportData/oneGene/background_MB-E10-5_chr1_genes_Eya1_interactions.bigwig" ftype="bigwig" compare="sim_size" /> | 144 <element name="background_MB-E10-5_chr1_genes_Eya1_interactions.bigwig" file="cHi-C/chicExportData/oneGene/background_MB-E10-5_chr1_genes_Eya1_interactions.bigwig" ftype="bigwig" compare="sim_size" /> |
| 141 <element name="FL-E13-5_chr1_genes_Eya1.bigwig" file="cHi-C/chicExportData/oneGene/FL-E13-5_chr1_genes_Eya1.bigwig" ftype="bigwig" compare="sim_size" /> | |
| 142 <element name="MB-E10-5_chr1_genes_Eya1.bigwig" file="cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1.bigwig" ftype="bigwig" compare="sim_size" /> | |
| 143 </output_collection> | 145 </output_collection> |
| 144 </test> | 146 </test> |
| 145 <test expect_num_outputs="2"> | 147 <test expect_num_outputs="2"> |
| 146 <param name="file" value="cHi-C/chicViewpoint/two_matrices.hdf5" /> | 148 <param name="file" value="cHi-C/chicViewpoint/two_matrices.hdf5" /> |
| 147 <conditional name="fileType_conditional"> | 149 <conditional name="fileType_conditional"> |