deeptools_compute_matrix: computeMatrix.xml comparison

comparison computeMatrix.xml @ 7:021729469baf draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69

author	bgruening
date	Wed, 23 Dec 2015 07:34:34 -0500
parents	451e73bf38fe
children	e3f4303309cc

comparison

equal deleted inserted replaced

-:451e73bf38fe
+:021729469baf
 <tool id="deeptools_compute_matrix" name="computeMatrix" version="@WRAPPER_VERSION@.0">
-<description>preparation step to plot a heatmap or a profile</description>
+<description>prepares data for plotting a heatmap or a profile of given regions</description>
 <macros>
 <token name="@BINARY@">computeMatrix</token>
 <import>deepTools_macros.xml</import>
 </macros>
 <expand macro="requirements" />
 <command>
 <![CDATA[
 #import tempfile
-#for $rf in $regionsFiles:
-cat "$rf.regionsFile" >> ./temp_input_path;
-#if str($rf.label.value).strip():
-echo "\#$rf.label.value" >> ./temp_input_path;
-#else:
-echo "\#$rf.regionsFile.name" >> ./temp_input_path;
-#end if
-#end for
 @BINARY@
 $mode.mode_select
---regionsFileName ./temp_input_path
+--regionsFileName
---scoreFileName '$scoreFile'
+#for $rf in $regionsFiles:
+'$rf.regionsFile'
+#end for
+--scoreFileName
+#for $bw in $scoreFileName:
+'$bw'
+#end for
 --outFileName '$outFileName'
 @THREADS@
 #if $output.showOutputSettings == "yes"
-#if $output.saveData:
---outFileNameData '$outFileNameData'
-#end if
 #if $output.saveMatrix:
 --outFileNameMatrix '$outFileNameMatrix'
 #end if
 #if $output.saveSortedRegions:
 $mode.nanAfterEnd
 --beforeRegionStartLength $mode.beforeRegionStartLength
 --afterRegionStartLength $mode.afterRegionStartLength
 #else
 --regionBodyLength $mode.regionBodyLength
---startLabel "$mode.startLabel"
---endLabel "$mode.endLabel"
 #if $mode.regionStartLength.regionStartLength_select == "yes":
 --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength
 --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength
 #end if
 #end if
 #end if
 ]]>
 </command>
 <inputs>
-<repeat name="regionsFiles" title="regions to plot" min="1">
+<repeat name="regionsFiles" title="Select regions" min="1">
 <param name="regionsFile" format="bed" type="data" label="Regions to plot"
 help="File, in BED format, containing the regions to plot."/>
-<param name="label" type="text" size="30" optional="true" value="" label="Label"
-help="Label to use in the output."/>
 </repeat>
-<param name="scoreFile" format="bigwig" type="data"
+<param name="scoreFileName" format="bigwig" type="data"
-label="Score file"
+label="Score file" multiple="True"
 help="Should be a bigWig file (containing a score, usually covering
 the whole genome). You can generate a bigWig file either from a
 bedGraph or WIG file using UCSC tools or from a BAM file using the
-deepTool bamCoverage. (-scoreFile)"/>
+deepTool bamCoverage. (--scoreFileName)"/>
 <conditional name="mode" >
 <param name="mode_select" type="select"
 label="computeMatrix has two main output options"
 help="In the scale-regions mode, all regions in the BED file are
 stretched or shrunk to the same length (bp) that is indicated
 by the user. Reference-point refers to a position within the BED
 regions (e.g start of region). In the reference-point mode only
 those genomic positions before (downstream) and/or after (upstream)
-the reference point will be plotted.">
+the reference point will be considered.">
 <option value="scale-regions" selected="true">scale-regions</option>
 <option value="reference-point">reference-point</option>
 </param>
 <when value="scale-regions" >
 <param argument="--regionBodyLength" type="integer" value="500"
 label="Distance in bp to which all regions are going to be fitted" help=""/>
-<param argument="--startLabel" type="text" value="TSS" size="10"
-label="Label for the region start"
-help ="Label shown in the plot for the start of the region.
-Default is TSS (transcription start site), but could be changed to anything,
-e.g. &quot;peak start&quot;." />
-<param argument="--endLabel" type="text" value="TES" size="10"
-label="Label for the region end"
-help="Label shown in the plot for the region end. Default is TES (transcription end site)."/>
 <conditional name="regionStartLength">
 <param name="regionStartLength_select" type="select" label="Set distance up- and downstream of the given regions">
 <option value="no" selected="true">no</option>
 <option value="yes">yes</option>
 </param>
 <param name="missingDataAsZero" type="boolean" truevalue="--missingDataAsZero" falsevalue="" checked="False"
 label="Convert missing values to 0?."
 help="If set to 'yes', missing values (NAs) are converted to 0.
 The default is to ignore such cases, which will be
-depicted as black areas in the heatmap by default." />
+depicted as black areas once a heatmap is created." />
 <expand macro="skipZeros" />
 <expand macro="skipNAs" />
 <param name="minThreshold" type="float" optional="True"
 <data format="deeptools_compute_matrix_archive" name="outFileName" label="${tool.name} on ${on_string}: Matrix" />
 <expand macro="output_graphic_outputs" />
 <expand macro="output_save_matrix_values" />
 </outputs>
 <!--
 computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1
 -->
 <tests>
 <test>
 <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" />
-<param name="scoreFile" value="bamCoverage_result4.bw" ftype="bigwig" />
+<param name="scoreFileName" value="bamCoverage_result4.bw" ftype="bigwig" />
 <param name="showAdvancedOpt" value="yes" />
 <param name="mode_select" value="reference-point" />
 <param name="binSize" value="10" />
 <param name="sortUsing" value="sum" />
 <param name="averageTypeBins" value="sum" />
 <param name="afterRegionStartLength" value="10" />
 <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
 </test>
 <test>
 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
-<param name="scoreFile" value="computeMatrix2.bw" ftype="bigwig" />
+<param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" />
 <param name="showAdvancedOpt" value="yes" />
 <param name="mode_select" value="reference-point" />
 <param name="binSize" value="10" />
 <param name="beforeRegionStartLength" value="10" />
 <param name="afterRegionStartLength" value="10" />
 <output name="outFileName" file="computeMatrix_result2.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
 </test>
 <test>
 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
-<param name="scoreFile" value="computeMatrix2.bw" ftype="bigwig" />
+<param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" />
 <param name="showAdvancedOpt" value="yes" />
 <param name="mode_select" value="scale-regions" />
 <param name="endLabel" value="END" />
 <param name="regionStartLength" value="yes" />
 <output name="outFileName" file="computeMatrix_result3.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
 .. image:: $PATH_TO_IMAGES/flowChart_computeMatrixetc.png
 :alt: Relationship between computeMatrix, heatmapper and profiler
-You can find more details on the computeMatrix wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-computeMatrix
+You can find more details on the computeMatrix doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/computeMatrix.html
 -----
 @REFERENCES@

Mercurial > repos > bgruening > deeptools_compute_matrix

comparison computeMatrix.xml @ 7:021729469baf draft