Mercurial > repos > iuc > macs2
diff macs2_callpeak.xml @ 14:c16dbe4e2db2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit c9c5c4dd15aed950ed9b43a294ce6c41f5732a23
| author | iuc |
|---|---|
| date | Mon, 06 Aug 2018 10:41:57 -0400 |
| parents | 01cded2297b7 |
| children | c33686854b19 |
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--- a/macs2_callpeak.xml Fri May 04 21:39:56 2018 -0400 +++ b/macs2_callpeak.xml Mon Aug 06 10:41:57 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.3" profile="17.09"> +<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.4" profile="17.09"> <description>Call peaks from alignment results</description> <macros> <import>macs2_macros.xml</import> @@ -8,21 +8,25 @@ <expand macro="stdio" /> <expand macro="version_command" /> <command><![CDATA[ + #import re + @home_dir@ - #set $temp_stderr = 'macs2_stderr' + (macs2 callpeak - --name 'MACS2' - ## Treatment File(s) #if str($treatment.t_multi_select) == "Yes": -t ${ ' '.join( [ "'%s'" % $x for $x in $treatment.input_treatment_file] ) } + #set identifier = re.sub('[^\w\-]', '_', str($treatment.input_treatment_file[0].element_identifier)) #else -t '$treatment.input_treatment_file' + #set identifier = re.sub('[^\w\-]', '_', str($treatment.input_treatment_file.element_identifier)) #end if + --name $identifier + ## Control File(s) #if str($control.c_select) == "Yes": @@ -98,24 +102,24 @@ 2>&1 > $temp_stderr) #if "peaks_tabular" in str($outputs).split(','): && - cp MACS2_peaks.xls '${ output_tabular }' + cp ${identifier}_peaks.xls '${ output_tabular }' #end if ## run R to create pdf from model script #if $nomodel_type.nomodel_type_selector == "create_model" and "pdf" in str($outputs).split(',') and $format != "BAMPE": && - Rscript MACS2_model.r > MACS2_model.r.log + Rscript ${identifier}_model.r > ${identifier}_model.r.log #end if #if 'html' in str($outputs).split(','): ## if output files exists, move them to the files_path and create a html result page linking to them && ( - count=`ls -1 MACS2* 2>/dev/null | wc -l`; + count=`ls -1 ${identifier}* 2>/dev/null | wc -l`; if [ \$count != 0 ]; then mkdir '${ output_extra_files.files_path }' && - cp -r MACS2* '${ output_extra_files.files_path }' && + cp -r ${identifier}* '${ output_extra_files.files_path }' && python '$__tool_directory__/dir2html.py' '${ output_extra_files.files_path }' $temp_stderr > '${ output_extra_files }'; fi; @@ -202,7 +206,7 @@ </conditional> <param name="outputs" type="select" display="checkboxes" multiple="True" optional="True" label="Additional Outputs" help="PDF is only created when the model is built"> - <option value="peaks_tabular">Peaks as tabular file</option> + <option value="peaks_tabular">Peaks as tabular file (compatible wih MultiQC)</option> <option value="summits">Peak summits</option> <option value="bdg" >Scores in bedGraph files (--bdg)</option> <option value="html">Summary page (html)</option> @@ -246,31 +250,31 @@ <data name="output_tabular" format="tabular" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Peaks in tabular format)"> <filter> outputs and 'peaks_tabular' in outputs</filter> </data> - <data name="output_broadpeaks" format="bed" from_work_dir="MACS2_peaks.broadPeak" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (broad Peaks)"> + <data name="output_broadpeaks" format="bed" from_work_dir="*_peaks.broadPeak" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (broad Peaks)"> <filter> (( advanced_options['broad_options']['broad_options_selector'] == "broad" )) </filter> </data> - <data name="output_gappedpeaks" format="bed" from_work_dir="MACS2_peaks.gappedPeak" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (gapped Peaks)"> + <data name="output_gappedpeaks" format="bed" from_work_dir="*_peaks.gappedPeak" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (gapped Peaks)"> <filter> (( advanced_options['broad_options']['broad_options_selector'] == "broad" )) </filter> </data> - <data name="output_narrowpeaks" format="bed" from_work_dir="MACS2_peaks.narrowPeak" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (narrow Peaks)"> + <data name="output_narrowpeaks" format="bed" from_work_dir="*_peaks.narrowPeak" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (narrow Peaks)"> <filter> (( advanced_options['broad_options']['broad_options_selector'] == "nobroad" )) </filter> </data> - <data name="output_summits" format="bed" from_work_dir="MACS2_summits.bed" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (summits in BED)"> + <data name="output_summits" format="bed" from_work_dir="*_summits.bed" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (summits in BED)"> <filter>outputs and 'summits' in outputs</filter> </data> - <data name="output_plot" format="pdf" from_work_dir="MACS2_model.pdf" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (plot)"> + <data name="output_plot" format="pdf" from_work_dir="*_model.pdf" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (plot)"> <filter> (( outputs and 'pdf' in outputs and @@ -279,10 +283,10 @@ )) </filter> </data> - <data name="output_treat_pileup" format="bedgraph" from_work_dir="MACS2_treat_pileup.bdg" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Bedgraph Treatment)"> + <data name="output_treat_pileup" format="bedgraph" from_work_dir="*_treat_pileup.bdg" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Bedgraph Treatment)"> <filter>outputs and 'bdg' in outputs</filter> </data> - <data name="output_control_lambda" format="bedgraph" from_work_dir="MACS2_control_lambda.bdg" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Bedgraph Control)"> + <data name="output_control_lambda" format="bedgraph" from_work_dir="*_control_lambda.bdg" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (Bedgraph Control)"> <filter>outputs and 'bdg' in outputs</filter> </data> <data name="output_extra_files" format="html" default_identifier_source="treatment|input_treatment_file" label="${tool.name} on ${on_string} (html report)"> @@ -305,7 +309,7 @@ <param name="upper" value="50" /> <output name="output_control_lambda" compare="contains" file="callpeak_control_part.bdg" lines_diff="1"/> <output name="output_treat_pileup" compare="contains" file="callpeak_treatment_part.bdg" lines_diff="1"/> - <output name="output_tabular" compare="contains" file="callpeak_part.tabular" lines_diff="1"/> + <output name="output_tabular" compare="contains" file="callpeak_part.tabular" lines_diff="3"/> <output name="output_extra_files"> <assert_contents> <has_text text="Additional output created by MACS2" /> @@ -379,7 +383,7 @@ This tool produces a BED file of narrowPeaks as default output. It can also produce additional outputs, which can be selected under the **Additional Outputs** option above. * **a BED file of peaks** (default) - * a tabular file of peaks + * a tabular file of peaks (compatible wih MultiQC) * a BED file of peak summits * two bedGraph files of scores, for treatment pileup and control lambda * a HTML summary page @@ -396,9 +400,9 @@ ======= ========= ======= ============ ==== === ======= ======== ======= ======= 1 2 3 4 5 6 7 8 9 **10** ======= ========= ======= ============ ==== === ======= ======== ======= ======= - chr1 840081 840400 MACS2_peak_1 69 . 4.89872 10.50944 6.91052 158 - chr1 919419 919785 MACS2_peak_2 87 . 5.85158 12.44148 8.70936 130 - chr1 937220 937483 MACS2_peak_3 66 . 4.87632 10.06728 6.61759 154 + chr1 840081 840400 treat1_peak_1 69 . 4.89872 10.50944 6.91052 158 + chr1 919419 919785 treat1_peak_2 87 . 5.85158 12.44148 8.70936 130 + chr1 937220 937483 treat1_peak_3 66 . 4.87632 10.06728 6.61759 154 ======= ========= ======= ============ ==== === ======= ======== ======= ======= Columns contain the following data: @@ -417,16 +421,16 @@ **Peaks tabular File** -A tabular file which contains information about called peaks. You can open it in Excel and sort/filter using Excel functions. +A tabular file which contains information about called peaks. You can open it in Excel and sort/filter using Excel functions. This file is compatible with **MultiQC**. Example: ======= ========= ======= ========== ============== ========== ================== =================== ================== ============= **chr** **start** **end** **length** **abs_summit** **pileup** **-log10(pvalue)** **fold_enrichment** **-log10(qvalue)** **name** ======= ========= ======= ========== ============== ========== ================== =================== ================== ============= - chr1 840082 840400 319 840240 4.00 10.50944 4.89872 6.91052 MACS2_peak_1 - chr1 919420 919785 366 919550 5.00 12.44148 5.85158 8.70936 MACS2_peak_2 - chr1 937221 937483 263 937375 4.00 10.06728 4.87632 6.61759 MACS2_peak_3 + chr1 840082 840400 319 840240 4.00 10.50944 4.89872 6.91052 treat1_peak_1 + chr1 919420 919785 366 919550 5.00 12.44148 5.85158 8.70936 treat1_peak_2 + chr1 937221 937483 263 937375 4.00 10.06728 4.87632 6.61759 treat1_peak_3 ======= ========= ======= ========== ============== ========== ================== =================== ================== ============= Columns contain the following data: @@ -454,9 +458,9 @@ ======= ========= ======= ============ ======= 1 2 3 4 **5** ======= ========= ======= ============ ======= - chr1 840239 840240 MACS2_peak_1 6.91052 - chr1 919549 919550 MACS2_peak_2 8.70936 - chr1 937374 937375 MACS2_peak_3 6.61759 + chr1 840239 840240 treat1_peak_1 6.91052 + chr1 919549 919550 treat1_peak_2 8.70936 + chr1 937374 937375 treat1_peak_3 6.61759 ======= ========= ======= ============ ======= Columns contain the following data: @@ -513,9 +517,9 @@ ======= ========= ======= ============ ==== === ======= ======= ======= 1 2 3 4 5 6 7 8 9 ======= ========= ======= ============ ==== === ======= ======= ======= - chr1 840081 840400 MACS2_peak_1 52 . 4.08790 8.57605 5.21506 - chr1 919419 919785 MACS2_peak_2 56 . 4.37270 8.90436 5.60462 - chr1 937220 937483 MACS2_peak_3 48 . 4.02343 8.06676 4.86861 + chr1 840081 840400 treat1_peak_1 52 . 4.08790 8.57605 5.21506 + chr1 919419 919785 treat1_peak_2 56 . 4.37270 8.90436 5.60462 + chr1 937220 937483 treat1_peak_3 48 . 4.02343 8.06676 4.86861 ======= ========= ======= ============ ==== === ======= ======= ======= @@ -541,9 +545,9 @@ ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= ======= 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= ======= - chr1 840081 840400 MACS2_peak_1 52 . 840081 840400 0 1 319 0 4.08790 8.57605 5.21506 - chr1 919419 919785 MACS2_peak_2 56 . 919419 919785 0 1 366 0 4.37270 8.90436 5.60462 - chr1 937220 937483 MACS2_peak_3 48 . 937220 937483 0 1 263 0 4.02343 8.06676 4.86861 + chr1 840081 840400 treat1_peak_1 52 . 840081 840400 0 1 319 0 4.08790 8.57605 5.21506 + chr1 919419 919785 treat1_peak_2 56 . 919419 919785 0 1 366 0 4.37270 8.90436 5.60462 + chr1 937220 937483 treat1_peak_3 48 . 937220 937483 0 1 263 0 4.02343 8.06676 4.86861 ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= ======= Columns contain the following data: