macs2: macs2_callpeak.xml comparison

comparison 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

comparison

equal deleted inserted replaced

-:01cded2297b7
+:c16dbe4e2db2
-<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>
 </macros>
 <expand macro="requirements">
 </expand>
 <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":
 #if str($control.c_multiple.c_multi_select) == "Yes":
 #end if
 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;
 )
 #end if
 <param name="qvalue" type="float" value="0.05" label="Minimum FDR (q-value) cutoff for peak detection" help="The q-value (minimum FDR) cutoff to call significant regions. Default is 0.05. For broad marks, you can try 0.05 as cutoff. Q-values are calculated from p-values using Benjamini-Hochberg procedure. (--qvalue)"/>
 </when>
 </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>
 <option value="pdf">Plot in PDF (only available if a model is created and if BAMPE is not used)</option>
 </param>
 <outputs>
 <!--callpeaks output-->
 <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 ${on_string} (plot)">
 <filter>
 ((
 outputs and 'pdf' in outputs and
 nomodel_type['nomodel_type_selector'] == "create_model" and
 format != "BAMPE"
 ))
 </filter>
 </data>
-<data name="output_treat_pileup" format="bedgraph" from_work_dir="MACS2_treat_pileup.bdg" default_identifier_source="treatment|input_treatment_file" label="${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)">
 <filter>outputs and 'html' in outputs</filter>
 </data>
 <param name="gsize" value="3300000000" />
 <param name="lower" value="5" />
 <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" />
 </assert_contents>
 </output>
 **Outputs**
 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
 * a PDF plot (if model is built)
 * a BED file of broad peaks (if **Composite broad regions** is selected under Advanced Options)
 Example:
 ======= ========= ======= ============ ==== === ======= ======== ======= =======
 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    840081    840400  treat1_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    919419    919785  treat1_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    937220    937483  treat1_peak_3  66   .  4.87632 10.06728 6.61759 154
 ======= ========= ======= ============ ==== === ======= ======== ======= =======
 Columns contain the following data:
 * **1st**: chromosome name
 * **10th**: relative summit position to peak start
 **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    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             MACS2_peak_2
+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             MACS2_peak_3
+chr1    937221    937483  263        937375         4.00       10.06728            4.87632             6.61759             treat1_peak_3
 ======= ========= ======= ========== ============== ========== ==================  =================== ================== =============
 Columns contain the following data:
 * **chr**: chromosome name
 Example:
 ======= ========= ======= ============ =======
 1          2        3          4        **5**
 ======= ========= ======= ============ =======
-chr1    840239    840240  MACS2_peak_1 6.91052
+chr1    840239    840240  treat1_peak_1 6.91052
-chr1    919549    919550  MACS2_peak_2 8.70936
+chr1    919549    919550  treat1_peak_2 8.70936
-chr1    937374    937375  MACS2_peak_3 6.61759
+chr1    937374    937375  treat1_peak_3 6.61759
 ======= ========= ======= ============ =======
 Columns contain the following data:
 * **1st**: chromosome name
 Example:
 ======= ========= ======= ============ ==== === ======= ======= =======
 1        2         3       4            5    6   7       8       9
 ======= ========= ======= ============ ==== === ======= ======= =======
-chr1    840081    840400  MACS2_peak_1  52   .  4.08790 8.57605 5.21506
+chr1    840081    840400  treat1_peak_1  52   .  4.08790 8.57605 5.21506
-chr1    919419    919785  MACS2_peak_2  56   .  4.37270 8.90436 5.60462
+chr1    919419    919785  treat1_peak_2  56   .  4.37270 8.90436 5.60462
-chr1    937220    937483  MACS2_peak_3  48   .  4.02343 8.06676 4.86861
+chr1    937220    937483  treat1_peak_3  48   .  4.02343 8.06676 4.86861
 ======= ========= ======= ============ ==== === ======= ======= =======
 Columns contain the following data:
 Example:
 ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= =======
 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    840081    840400  treat1_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    919419    919785  treat1_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    937220    937483  treat1_peak_3  48   .  937220  937483   0   1  263  0  4.02343 8.06676 4.86861
 ======= ========= ======= ============ ==== === ======= ======= === === === === ======= ======= =======
 Columns contain the following data:
 * **1st**: chromosome name

Mercurial > repos > iuc > macs2

comparison macs2_callpeak.xml @ 14:c16dbe4e2db2 draft