# HG changeset patch
# User iuc
# Date 1521726217 14400
# Node ID 38769345062e9ee97576863dcb6bf250bebd7d28
# Parent  cb785e26207cf2e36c67e7edbc997de08547b221
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 09ef7ee96fadeef22273029ea23d1e140ce96737

diff -r cb785e26207c -r 38769345062e macs2_bdgdiff.xml
--- a/macs2_bdgdiff.xml	Tue Mar 06 07:25:31 2018 -0500
+++ b/macs2_bdgdiff.xml	Thu Mar 22 09:43:37 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="macs2_bdgdiff" name="MACS2 bdgdiff" version="@VERSION_STRING@.0">
+<tool id="macs2_bdgdiff" name="MACS2 bdgdiff" version="@VERSION_STRING@.1" profile="17.09">
     <description>Differential peak detection based on paired four bedgraph files</description>
     <macros>
         <import>macs2_macros.xml</import>
@@ -23,7 +23,7 @@
             -o c1.bed c2.bed both.bed &&
 
             awk '!/^track name/' "c1.bed" > '${ output_cond1 }' &&
-            awk '!/^track name/' "c2.bed" > '${ output_cond1 }' &&
+            awk '!/^track name/' "c2.bed" > '${ output_cond2 }' &&
             awk '!/^track name/' "both.bed" > '${ output_both }'
     ]]></command>
     <inputs>
@@ -51,7 +51,6 @@
     </outputs>
     <tests>
         <test>
-
             <param name="t1" value="bdgdiff_t1.bdg" ftype="bedgraph"/>
             <param name="t2" value="bdgdiff_t2.bdg" ftype="bedgraph"/>
             <param name="c1" value="bdgdiff_c1.bdg" ftype="bedgraph"/>
@@ -61,11 +60,13 @@
             <param name="depth1" value="10"/>
             <param name="depth2" value="1"/>
             <param name="maxgap" value="100"/>
-            <output name="output_cond1">
+            <output name="output_cond1" ftype="bed" value="bdgdiff_output_c1.bed"/>
+            <output name="output_cond2">
                 <assert_contents>
                     <has_text text="c2.bed1" />
                 </assert_contents>
             </output>
+            <output name="output_both" ftype="bed" value="bdgdiff_output_both.bed"/>
         </test>
     </tests>
     <help>
diff -r cb785e26207c -r 38769345062e macs2_callpeak.xml
--- a/macs2_callpeak.xml	Tue Mar 06 07:25:31 2018 -0500
+++ b/macs2_callpeak.xml	Thu Mar 22 09:43:37 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.3">
+<tool id="macs2_callpeak" name="MACS2 callpeak" version="@VERSION_STRING@.3" profile="17.09">
     <description>Call peaks from alignment results</description>
     <macros>
         <import>macs2_macros.xml</import>
@@ -243,34 +243,34 @@
     </inputs>
     <outputs>
         <!--callpeaks output-->
-        <data name="output_tabular" format="tabular" label="${tool.name} on ${on_string} (Peaks in tabular format)">
+        <data name="output_tabular" format="tabular" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (Peaks in tabular format)">
             <filter> outputs and 'peaks_tabular' in outputs</filter>
         </data>
-        <data name="output_broadpeaks" format="bed" from_work_dir="MACS2_peaks.broadPeak" label="${tool.name} on ${on_string} (broad Peaks)">
+        <data name="output_broadpeaks" format="bed" from_work_dir="MACS2_peaks.broadPeak" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (broad Peaks)">
             <filter>
             ((
               advanced_options['broad_options']['broad_options_selector'] == "broad"
             ))
             </filter>
         </data>
-        <data name="output_gappedpeaks" format="bed" from_work_dir="MACS2_peaks.gappedPeak" label="${tool.name} on ${on_string} (gapped Peaks)">
+        <data name="output_gappedpeaks" format="bed" from_work_dir="MACS2_peaks.gappedPeak" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (gapped Peaks)">
             <filter>
             ((
               advanced_options['broad_options']['broad_options_selector'] == "broad"
             ))
             </filter>
         </data>
-        <data name="output_narrowpeaks" format="bed" from_work_dir="MACS2_peaks.narrowPeak" label="${tool.name} on ${on_string} (narrow Peaks)">
+        <data name="output_narrowpeaks" format="bed" from_work_dir="MACS2_peaks.narrowPeak" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (narrow Peaks)">
             <filter>
             ((
               advanced_options['broad_options']['broad_options_selector'] == "nobroad"
             ))
             </filter>
         </data>
-        <data name="output_summits" format="bed" from_work_dir="MACS2_summits.bed" label="${tool.name} on ${on_string} (summits in BED)">
+        <data name="output_summits" format="bed" from_work_dir="MACS2_summits.bed" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (summits in BED)">
             <filter>outputs and 'summits' in outputs</filter>
         </data>
-        <data name="output_plot" format="pdf" from_work_dir="MACS2_model.pdf" label="${tool.name} on ${on_string} (plot)">
+        <data name="output_plot" format="pdf" from_work_dir="MACS2_model.pdf" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (plot)">
             <filter>
             ((
               outputs and 'pdf' in outputs and
@@ -279,13 +279,13 @@
             ))
             </filter>
         </data>
-        <data name="output_treat_pileup" format="bedgraph" from_work_dir="MACS2_treat_pileup.bdg" label="${tool.name} on ${on_string} (Bedgraph Treatment)">
+        <data name="output_treat_pileup" format="bedgraph" from_work_dir="MACS2_treat_pileup.bdg" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (Bedgraph Treatment)">
             <filter>outputs and 'bdg' in outputs</filter>
         </data>
-        <data name="output_control_lambda" format="bedgraph" from_work_dir="MACS2_control_lambda.bdg" label="${tool.name} on ${on_string} (Bedgraph Control)">
+        <data name="output_control_lambda" format="bedgraph" from_work_dir="MACS2_control_lambda.bdg" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (Bedgraph Control)">
             <filter>outputs and 'bdg' in outputs</filter>
         </data>
-        <data name="output_extra_files" format="html" label="${tool.name} on ${on_string} (html report)">
+        <data name="output_extra_files" format="html" default_identifier_source="input_treatment_file" label="${tool.name} on ${on_string} (html report)">
             <filter>outputs and 'html' in outputs</filter>
         </data>
     </outputs>
@@ -349,8 +349,6 @@
 
 **callpeak** is the main function of the MACS2_ package. MACS identifies enriched binding sites in ChIP-seq experiments. It captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation.
 
-.. _MACS2: https://github.com/taoliu/MACS
-
 -----
 
 **Inputs**
@@ -372,6 +370,8 @@
  ce: 9e7
  dm: 1.2e8
 
+Or see the **deepTools** website for updated information on calculating `Effective Genome Size`_.
+
 -----
 
 **Outputs**
@@ -587,6 +587,8 @@
 
 If MACS2 fails, it is usually because it cannot build the model for peaks. You may want to extend **mfold** range by increasing the upper bound or play with **Build model** options. For more information, see the MACS2_ website.
 
+.. _MACS2: https://github.com/taoliu/MACS
+.. _`Effective Genome Size`: http://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html
 .. _`UCSC website here`: https://genome.ucsc.edu/goldenPath/help/bedgraph.html
 
 @citation@
diff -r cb785e26207c -r 38769345062e test-data/bdgdiff_output_both.bed
diff -r cb785e26207c -r 38769345062e test-data/bdgdiff_output_c1.bed
diff -r cb785e26207c -r 38769345062e test-data/bdgdiff_output_c2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bdgdiff_output_c2.bed	Thu Mar 22 09:43:37 2018 -0400
@@ -0,0 +1,1 @@
+chrV	6194	6538	c2.bed1	7.25269