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changeset 44:03cec12dafc3 draft default tip

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"planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b"
author iuc
date Sun, 22 Dec 2019 17:11:12 +0000
parents 61f2dedb6b85
children
files .shed.yml macros.xml multigps.xml test-data/hg19_all_events_table1.tabular test-data/hg19_all_events_table2.tabular test-data/hg19_output_bed1.bed test-data/hg19_output_bed2.bed test-data/hg19_output_html1.html test-data/hg19_output_html2.html test-data/hg19_replicates_counts1.tabular test-data/hg19_replicates_counts2.tabular tool-data/hg19.len
diffstat 12 files changed, 59 insertions(+), 61 deletions(-) [+]
line wrap: on
line diff
--- a/.shed.yml	Thu Apr 06 11:26:41 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
-name: multigps
-owner: iuc
-description: Analyzes collections of multi-condition ChIP-seq data.
-homepage_url: http://mahonylab.org/software/multigps/
-long_description: |
-  Contains a tool that runs MultiGPS, a framework for analyzing collections of multi-condition ChIP-seq
-  datasets and characterizing differential binding events between conditions.  MultiGPS encourages consistency
-  in the reported binding event locations across conditions and provides accurate estimation of ChIP enrichment
-  levels at each event.  MultiGPS loads all data to memory, so you will need a lot of available memory if you
-  are running analysis over many conditions or large datasets.
-type: unrestricted
-categories:
-- ChIP-seq
--- a/macros.xml	Thu Apr 06 11:26:41 2017 -0400
+++ b/macros.xml	Sun Dec 22 17:11:12 2019 +0000
@@ -1,16 +1,5 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <macros>
-    <xml name="motif_finding_params">
-        <param name="memenmotifs" type="integer" min="0" value="3" label="Number of motifs MEME should find for each condition" />
-        <param name="mememinw" type="integer" min="0" value="6" label="Minimum motif width for MEME" />
-        <param name="mememaxw" type="integer" min="0" value="16" label="Maximum motif width for MEME" />
-    </xml>
-    <xml name="param_experiment_type">
-        <param name="experiment_type" type="select" display="radio" label="Experiment type for this replicate">
-            <option value="chipseq" selected="True">ChIP-seq</option>
-            <option value="chipexo">ChIP-exo</option>
-        </param>
-    </xml>
     <xml name="cond_fixedreadcount">
         <conditional name="fixedreadcount_cond">
             <param  name="fixedreadcount_select" type="select" label="Set fixed per-base read count limit for this replicate?" help="Selecting No uses a global per-base limit that is estimated from a Poisson distribution.">
@@ -23,4 +12,22 @@
             </when>
         </conditional>
     </xml>
+    <xml name="param_experiment_type">
+        <param name="experiment_type" type="select" display="radio" label="Experiment type for this replicate">
+            <option value="chipseq" selected="True">ChIP-seq</option>
+            <option value="chipexo">ChIP-exo</option>
+        </param>
+    </xml>
+    <xml name="motif_finding_params">
+        <param name="memenmotifs" type="integer" min="0" value="3" label="Number of motifs MEME should find for each condition" />
+        <param name="mememinw" type="integer" min="0" value="6" label="Minimum motif width for MEME" />
+        <param name="mememaxw" type="integer" min="0" value="16" label="Maximum motif width for MEME" />
+    </xml>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="1">fonts-conda-ecosystem</requirement>
+            <requirement type="package" version="0.74">multigps</requirement>
+            <yield/>
+        </requirements>
+    </xml>
 </macros>
--- a/multigps.xml	Thu Apr 06 11:26:41 2017 -0400
+++ b/multigps.xml	Sun Dec 22 17:11:12 2019 +0000
@@ -3,9 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <requirements>
-        <requirement type="package" version="0.74">multigps</requirement>
-    </requirements>
+    <expand macro="requirements" />
     <command detect_errors="aggressive">
         <![CDATA[
             #set output_dir = $output_html.files_path
@@ -20,7 +18,11 @@
             ## Do not run the parallel version of meme.
             --meme1proc
             --threads \${GALAXY_SLOTS:-4}
-            --geninfo '$chromInfo'
+            #if str($in_test_mode) == "no":
+                --geninfo '$chromInfo'
+            #else:
+                --geninfo '$__tool_directory__/tool-data/hg19.len'
+            #end if
             ## Advanced options
             #set aoc = $advanced_options_cond
             #if str($aoc.advanced_options) == 'display':
@@ -410,6 +412,8 @@
             </when>
             <when value="hide" />
         </conditional>
+        <!-- Functional testing -->
+        <param name="in_test_mode" type="hidden" value="no" />
     </inputs>
     <outputs>
         <data name="output_design_file" format="tabular" label="${tool.name} (design file) on ${on_string}">
@@ -428,6 +432,7 @@
                 </repeat>
             </repeat>
             <param name="advanced_options" value="hide" />
+            <param name="in_test_mode" value="yes" />
             <output name="output_html" file="hg19_output_html1.html" ftype="html" compare="contains"/>
             <output name="output_bed" file="hg19_output_bed1.bed" ftype="bed"/>
             <output name="all_events_table" file="hg19_all_events_table1.tabular" ftype="tabular"/>
@@ -443,6 +448,7 @@
                 </repeat>
             </repeat>
             <param name="advanced_options" value="display" />
+            <param name="in_test_mode" value="yes" />
             <output name="output_html" file="hg19_output_html2.html" ftype="html" compare="contains"/>
             <output name="output_bed" file="hg19_output_bed2.bed" ftype="bed"/>
             <output name="all_events_table" file="hg19_all_events_table2.tabular" ftype="tabular"/>
@@ -466,7 +472,7 @@
 
 * **Loading data:**
 
- - **Optional file containing reads from a control experiment** - must be same format as input experiment
+ - **Optional file containing reads from a control experiment** - file containing reads from a control experiment
  - **Fixed per-base limit** - Fixed per-base limit (default: estimated from background model).
  - **Poisson threshold for filtering per base** - Look at neighboring positions to decide what the per-base limit should be.
  - **Use non-unique reads** - Use non-unique reads.
@@ -520,23 +526,7 @@
 
     </help>
     <citations>
-        <citation type="bibtex">
-            @article{Mahony2014,
-            journal = {PLOS Computational Biology},
-            author = {1. Mahony S, Edwards MD, Mazzoni EO, Sherwood RI, Kakumanu A, Morrison CA, Wichterle H, Gifford DK},
-            title = {An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding},
-            year = {2014},}
-            volume = {10},
-            number = {3},
-            pages = {e1003501},}
-        </citation>
-        <citation type="bibtex">
-            @article{Liang2012,
-            journal = {BMC Bioinformatics},
-            author = {2. Liang, Ketes},
-            title = {Normalization of ChIP-seq data with control},
-            year = {2012},}
-        </citation>
+        <citation type="doi">10.1371/journal.pcbi.1003501</citation>
     </citations>
 </tool>
 
--- a/test-data/hg19_all_events_table1.tabular	Thu Apr 06 11:26:41 2017 -0400
+++ b/test-data/hg19_all_events_table1.tabular	Sun Dec 22 17:11:12 2019 +0000
@@ -1,10 +1,10 @@
 ### MultiGPS output
 #Condition	Name	Index	TotalSigCount	SignalFraction
-#Condition	experiment	0	99.0	0.555
+#Condition	cond	0	99.0	0.555
 #Replicate	ParentCond	Name	Index	SigCount	CtrlCount	SigCtrlScaling	SignalFraction
-#Replicate	experiment	experiment:rep1	0	99.0	0	1	0.56
+#Replicate	cond	cond:1	0	99.0	0	1	0.56
 #
-#Point	experiment_Sig	experiment_Ctrl	experiment_log2Fold	experiment_log2P	ActiveConds
+#Point	cond_Sig	cond_Ctrl	cond_log2Fold	cond_log2P	ActiveConds
 chr1:569927	14.3	0.0	3.838	-6.470	1
 chr1:536042	1.0	0.0	0.014	-1.474	1
 chr1:535151	1.0	0.0	0.014	-1.413	1
--- a/test-data/hg19_all_events_table2.tabular	Thu Apr 06 11:26:41 2017 -0400
+++ b/test-data/hg19_all_events_table2.tabular	Sun Dec 22 17:11:12 2019 +0000
@@ -1,10 +1,10 @@
 ### MultiGPS output
 #Condition	Name	Index	TotalSigCount	SignalFraction
-#Condition	experiment	0	99.0	0.555
+#Condition	cond	0	99.0	0.555
 #Replicate	ParentCond	Name	Index	SigCount	CtrlCount	SigCtrlScaling	SignalFraction
-#Replicate	experiment	experiment:rep1	0	99.0	18.0	4.00	0.555
+#Replicate	cond	cond:1	0	99.0	18.0	4.00	0.555
 #
-#Point	experiment_Sig	experiment_Ctrl	experiment_log2Fold	experiment_log2P	ActiveConds
+#Point	cond_Sig	cond_Ctrl	cond_log2Fold	cond_log2P	ActiveConds
 chr1:569927	14.3	0.0	3.838	-6.470	1
 chr1:536042	1.0	0.0	0.014	-1.281	1
 chr1:535151	1.0	0.0	0.014	-1.211	1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hg19_output_bed1.bed	Sun Dec 22 17:11:12 2019 +0000
@@ -0,0 +1,1 @@
+track name=multiGPS-cond description=multiGPS events cond
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hg19_output_bed2.bed	Sun Dec 22 17:11:12 2019 +0000
@@ -0,0 +1,1 @@
+track name=multiGPS-cond description=multiGPS events cond
--- a/test-data/hg19_output_html1.html	Thu Apr 06 11:26:41 2017 -0400
+++ b/test-data/hg19_output_html1.html	Sun Dec 22 17:11:12 2019 +0000
@@ -1,13 +1,12 @@
 <html>
 	<body>
-</p>
 	<h2>Binding events</h2>
 	<table>
 		<tr>		<th>Condition</th>
 		<th>Events</th>
 		<th>File</th>
 		</tr>
-		<tr>		<td>experiment</td>
+		<tr>		<td>cond</td>
 		<td>0</td>
 		</tr>
 	</table>
@@ -19,7 +18,7 @@
 		<th>SignalFraction</th>
 		<th>ReadDistributionModel</th>
 		</tr>
-		<tr>		<td>experiment rep1</td>
+		<tr>		<td>cond 1</td>
 		<td>99.0</td>
 		<td>NA</td>
 		<td>0.555</td>
--- a/test-data/hg19_output_html2.html	Thu Apr 06 11:26:41 2017 -0400
+++ b/test-data/hg19_output_html2.html	Sun Dec 22 17:11:12 2019 +0000
@@ -1,13 +1,11 @@
 <html>
-	<body>
-</p>
 	<h2>Binding events</h2>
 	<table>
 		<tr>		<th>Condition</th>
 		<th>Events</th>
 		<th>File</th>
 		</tr>
-		<tr>		<td>experiment</td>
+		<tr>		<td>cond</td>
 		<td>0</td>
 		</tr>
 	</table>
@@ -19,7 +17,7 @@
 		<th>SignalFraction</th>
 		<th>ReadDistributionModel</th>
 		</tr>
-		<tr>		<td>experiment rep1</td>
+		<tr>		<td>cond 1</td>
 		<td>99.0</td>
 		<td>4.000</td>
 		<td>0.555</td>
--- a/test-data/hg19_replicates_counts1.tabular	Thu Apr 06 11:26:41 2017 -0400
+++ b/test-data/hg19_replicates_counts1.tabular	Sun Dec 22 17:11:12 2019 +0000
@@ -1,4 +1,4 @@
-Point	experiment:rep1
+Point	cond:1
 chr1:569927	14
 chr1:536042	1
 chr1:535151	1
--- a/test-data/hg19_replicates_counts2.tabular	Thu Apr 06 11:26:41 2017 -0400
+++ b/test-data/hg19_replicates_counts2.tabular	Sun Dec 22 17:11:12 2019 +0000
@@ -1,4 +1,4 @@
-Point	experiment:rep1
+Point	cond:1
 chr1:569927	14
 chr1:536042	1
 chr1:535151	1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/hg19.len	Sun Dec 22 17:11:12 2019 +0000
@@ -0,0 +1,15 @@
+chr1	249250621
+chr1_jh636052_fix	7283150
+chr1_jh636053_fix	1676126
+chr1_jh636054_fix	758378
+chr1_gl000192_random	547496
+chr1_gl383520_alt	366579
+chr1_gl383518_alt	182439
+chr1_gl949741_fix	151551
+chr1_gl383519_alt	110268
+chr1_gl000191_random	106433
+chr1_gl383517_fix	49352
+chr1_gl383516_fix	49316
+chr1_jh806575_fix	47409
+chr1_jh806573_fix	24680
+chr1_jh806574_fix	22982