changeset 41:9e2dc0d5082a draft default tip

planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9
author bgruening
date Thu, 01 Jun 2023 10:06:06 +0000
parents 6f2e93384b40
children
files deepTools_macros.xml plotPCA.xml readme.rst repository_dependencies.xml test-data/bigwigAverage2.bw test-data/multiBigwigSummary_result1.npz test-data/multiBigwigSummary_result2.npz test-data/multiBigwigSummary_result2.tabular test-data/test_compated.bw test-data/test_half.bw
diffstat 10 files changed, 250 insertions(+), 86 deletions(-) [+]
line wrap: on
line diff
--- a/deepTools_macros.xml	Fri Feb 11 09:53:45 2022 +0000
+++ b/deepTools_macros.xml	Thu Jun 01 10:06:06 2023 +0000
@@ -1,10 +1,11 @@
 <macros>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">3.5.1.0</token>
+    <token name="@TOOL_VERSION@">3.5.2</token>
+    <token name="@GALAXY_VERSION@">20.01</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.5.1">deeptools</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">deeptools</requirement>
             <requirement type="package" version="1.9">samtools</requirement>
         </requirements>
         <expand macro="stdio" />
@@ -368,7 +369,6 @@
     <xml name="pseudocount">
         <param argument="--pseudocount" type="text" value="1 1" label="Pseudocount" help="Small number to avoid dividing by zero. You can specify separate values for the pseudocount added to the numerator and denominator by providing two values separated by a space."/>
     </xml>
-
     <token name="@REFERENCES@">
 
 .. class:: infomark
@@ -483,7 +483,7 @@
     <token name="@multiple_input_bams@">
 <![CDATA[
         #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
-            #set custom_labels=labels
+            #set custom_labels=$custom_sample_labels_conditional.labels
         #end if
         #set files=[]
         #set labels=[]
@@ -498,7 +498,7 @@
                     ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' &&
                 #end if
                 #silent $files.append("'%s.bam'" % $counter)
-                #silent $labels.append("'%s'" % identifier)
+                #silent $labels.append("'%s'" % $identifier)
             #end for
         #else:
             #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
@@ -522,7 +522,7 @@
     <token name="@multiple_input_bigwigs@">
 <![CDATA[
         #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
-            #set custom_labels=labels
+            #set custom_labels=$custom_sample_labels_conditional.labels
         #end if
         #set files=[]
         #set labels=[]
--- a/plotPCA.xml	Fri Feb 11 09:53:45 2022 +0000
+++ b/plotPCA.xml	Thu Jun 01 10:06:06 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="deeptools_plot_pca" name="plotPCA" version="@WRAPPER_VERSION@.0" profile="18.01">
+<tool id="deeptools_plot_pca" name="plotPCA" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
     <description>Generate principal component analysis (PCA) plots from multiBamSummary or multiBigwigSummary output</description>
     <macros>
         <token name="@BINARY@">plotPCA</token>
@@ -78,7 +78,7 @@
             <param name="outFileFormat" value="png" />
             <param name="outFileNameData" value="True" />
             <output name="outFileName" file="plotPCA_result2.png" ftype="png" compare="sim_size" delta="12000" />
-            <output name="output_outFileNameData" file="plotPCA_result2.tabular" ftype="tabular" />
+            <output name="output_outFileNameData" file="plotPCA_result2.tabular" ftype="tabular" lines_diff="2" />
         </test>
     </tests>
     <help>
--- a/readme.rst	Fri Feb 11 09:53:45 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,74 +0,0 @@
-========================
-Galaxy deeptools wrapper
-========================
-
-deepTools are user-friendly tools for the normalization and visualization of 
-deep-sequencing data.
-They address the challenge of visualizing the large amounts of data that are now
-routinely generated from sequencing centers in a meaningful way. 
-To do so, deepTools contain useful routines to process the mapped reads data 
-through removal of duplicates and different filtering options to create coverage
-files in standard bedGraph and bigWig file formats. deepTools allow the creation
-of normalized coverage files or the comparison between two files 
-(for example, treatment and control). Finally, using such normalized and 
-standardized files, multiple visualizations can be created to identify 
-enrichments with functional annotations of the genome. 
-For a gallery of images that can be produced and a description 
-of the tools see our poster_.
-
-.. _poster: http://f1000.com/posters/browse/summary/1094053
-
-deeptools is developed under here:
-
-    https://github.com/deeptools/deepTools
-
-For support or questions please post to `Biostars <http://biostars.org>`__. For bug reports and feature requests please open an issue `<on github <http://github.com/deeptools/deeptools>`__.
-
-
-============
-Installation
-============
-
-Requirements: python-2.7
-
-Galaxy should be able to automatically install all other dependencies, such as numpy or scipy.
-
-For the best performance we recommend to install blas/lapack/atlas in your environment before
-installing deepTools from the Tool Shed.
-
-
-========
-Citation
-========
-
-deeptools are currently under review. In the meantime please refere to https://github.com/deeptools/deepTools.
-
-
-=======
-History
-=======
-
- * v1.0:        Initial public release
- * v1.5.8.2:    Include new citation tag, update version to 1.5.8.2 and change wrapper version
-
-
-Licence (MIT)
-=============
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in
-all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-THE SOFTWARE.
--- a/repository_dependencies.xml	Fri Feb 11 09:53:45 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-<?xml version="1.0" ?>
-<repositories>
-    <repository name="data_manager_twobit_builder" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" changeset_revision="b640d79b49cb"/>
-</repositories>
\ No newline at end of file
Binary file test-data/bigwigAverage2.bw has changed
Binary file test-data/multiBigwigSummary_result1.npz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiBigwigSummary_result2.npz	Thu Jun 01 10:06:06 2023 +0000
@@ -0,0 +1,121 @@
+#'chr'	'start'	'end'	'sample1'	'sample2'
+ch1	0	10	0.0	0.0
+ch1	10	20	0.0	0.0
+ch1	20	30	0.0	0.0
+ch1	30	40	0.0	0.0
+ch1	40	50	0.0	0.0
+ch1	50	60	0.0	0.0
+ch1	60	70	0.0	0.0
+ch1	70	80	0.0	0.0
+ch1	80	90	0.0	0.0
+ch1	90	100	0.0	0.0
+ch1	100	110	2.0	2.0
+ch1	110	120	2.0	2.0
+ch1	120	130	1.0	1.0
+ch1	130	140	0.0	0.0
+ch1	140	150	0.0	0.0
+ch1	150	160	0.0	0.0
+ch1	160	170	0.0	0.0
+ch1	170	180	0.0	0.0
+ch1	180	190	0.0	0.0
+ch1	190	200	0.0	0.0
+ch1	200	210	0.0	0.0
+ch1	210	220	0.0	0.0
+ch1	220	230	0.0	0.0
+ch1	230	240	0.0	0.0
+ch1	240	250	0.0	0.0
+ch1	250	260	0.0	0.0
+ch1	260	270	0.0	0.0
+ch1	270	280	0.0	0.0
+ch1	280	290	0.0	0.0
+ch1	290	300	0.0	0.0
+ch1	300	310	0.0	0.0
+ch1	310	320	0.0	0.0
+ch1	320	330	0.0	0.0
+ch1	330	340	0.0	0.0
+ch1	340	350	0.0	0.0
+ch1	350	360	0.0	0.0
+ch1	360	370	0.0	0.0
+ch1	370	380	0.0	0.0
+ch1	380	390	0.0	0.0
+ch1	390	400	0.0	0.0
+ch2	0	10	0.0	0.0
+ch2	10	20	0.0	0.0
+ch2	20	30	0.0	0.0
+ch2	30	40	0.0	0.0
+ch2	40	50	0.0	0.0
+ch2	50	60	3.0	3.0
+ch2	60	70	3.0	3.0
+ch2	70	80	1.5	1.5
+ch2	80	90	0.0	0.0
+ch2	90	100	0.0	0.0
+ch2	100	110	0.0	0.0
+ch2	110	120	0.0	0.0
+ch2	120	130	0.0	0.0
+ch2	130	140	0.0	0.0
+ch2	140	150	0.0	0.0
+ch2	150	160	1.0	1.0
+ch2	160	170	1.0	1.0
+ch2	170	180	0.5	0.5
+ch2	180	190	0.0	0.0
+ch2	190	200	0.0	0.0
+ch2	200	210	0.0	0.0
+ch2	210	220	0.0	0.0
+ch2	220	230	0.0	0.0
+ch2	230	240	0.0	0.0
+ch2	240	250	0.0	0.0
+ch2	250	260	0.0	0.0
+ch2	260	270	0.0	0.0
+ch2	270	280	0.0	0.0
+ch2	280	290	0.0	0.0
+ch2	290	300	0.0	0.0
+ch2	300	310	0.0	0.0
+ch2	310	320	0.0	0.0
+ch2	320	330	0.0	0.0
+ch2	330	340	0.0	0.0
+ch2	340	350	0.0	0.0
+ch2	350	360	0.0	0.0
+ch2	360	370	0.0	0.0
+ch2	370	380	0.0	0.0
+ch2	380	390	0.0	0.0
+ch2	390	400	0.0	0.0
+ch3	0	10	0.0	0.0
+ch3	10	20	0.0	0.0
+ch3	20	30	0.0	0.0
+ch3	30	40	0.0	0.0
+ch3	40	50	0.0	0.0
+ch3	50	60	3.0	3.0
+ch3	60	70	3.0	3.0
+ch3	70	80	1.5	1.5
+ch3	80	90	0.0	0.0
+ch3	90	100	0.0	0.0
+ch3	100	110	0.0	0.0
+ch3	110	120	0.0	0.0
+ch3	120	130	0.0	0.0
+ch3	130	140	0.0	0.0
+ch3	140	150	0.0	0.0
+ch3	150	160	1.0	1.0
+ch3	160	170	1.0	1.0
+ch3	170	180	0.5	0.5
+ch3	180	190	0.0	0.0
+ch3	190	200	0.0	0.0
+ch3	200	210	0.0	0.0
+ch3	210	220	0.0	0.0
+ch3	220	230	0.0	0.0
+ch3	230	240	0.0	0.0
+ch3	240	250	0.0	0.0
+ch3	250	260	0.0	0.0
+ch3	260	270	0.0	0.0
+ch3	270	280	0.0	0.0
+ch3	280	290	0.0	0.0
+ch3	290	300	0.0	0.0
+ch3	300	310	0.0	0.0
+ch3	310	320	0.0	0.0
+ch3	320	330	0.0	0.0
+ch3	330	340	0.0	0.0
+ch3	340	350	0.0	0.0
+ch3	350	360	0.0	0.0
+ch3	360	370	0.0	0.0
+ch3	370	380	0.0	0.0
+ch3	380	390	0.0	0.0
+ch3	390	400	0.0	0.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiBigwigSummary_result2.tabular	Thu Jun 01 10:06:06 2023 +0000
@@ -0,0 +1,121 @@
+#'chr'	'start'	'end'	'sample1'	'sample2'
+ch1	0	10	0.0	0.0
+ch1	10	20	0.0	0.0
+ch1	20	30	0.0	0.0
+ch1	30	40	0.0	0.0
+ch1	40	50	0.0	0.0
+ch1	50	60	0.0	0.0
+ch1	60	70	0.0	0.0
+ch1	70	80	0.0	0.0
+ch1	80	90	0.0	0.0
+ch1	90	100	0.0	0.0
+ch1	100	110	2.0	2.0
+ch1	110	120	2.0	2.0
+ch1	120	130	1.0	1.0
+ch1	130	140	0.0	0.0
+ch1	140	150	0.0	0.0
+ch1	150	160	0.0	0.0
+ch1	160	170	0.0	0.0
+ch1	170	180	0.0	0.0
+ch1	180	190	0.0	0.0
+ch1	190	200	0.0	0.0
+ch1	200	210	0.0	0.0
+ch1	210	220	0.0	0.0
+ch1	220	230	0.0	0.0
+ch1	230	240	0.0	0.0
+ch1	240	250	0.0	0.0
+ch1	250	260	0.0	0.0
+ch1	260	270	0.0	0.0
+ch1	270	280	0.0	0.0
+ch1	280	290	0.0	0.0
+ch1	290	300	0.0	0.0
+ch1	300	310	0.0	0.0
+ch1	310	320	0.0	0.0
+ch1	320	330	0.0	0.0
+ch1	330	340	0.0	0.0
+ch1	340	350	0.0	0.0
+ch1	350	360	0.0	0.0
+ch1	360	370	0.0	0.0
+ch1	370	380	0.0	0.0
+ch1	380	390	0.0	0.0
+ch1	390	400	0.0	0.0
+ch2	0	10	0.0	0.0
+ch2	10	20	0.0	0.0
+ch2	20	30	0.0	0.0
+ch2	30	40	0.0	0.0
+ch2	40	50	0.0	0.0
+ch2	50	60	3.0	3.0
+ch2	60	70	3.0	3.0
+ch2	70	80	1.5	1.5
+ch2	80	90	0.0	0.0
+ch2	90	100	0.0	0.0
+ch2	100	110	0.0	0.0
+ch2	110	120	0.0	0.0
+ch2	120	130	0.0	0.0
+ch2	130	140	0.0	0.0
+ch2	140	150	0.0	0.0
+ch2	150	160	1.0	1.0
+ch2	160	170	1.0	1.0
+ch2	170	180	0.5	0.5
+ch2	180	190	0.0	0.0
+ch2	190	200	0.0	0.0
+ch2	200	210	0.0	0.0
+ch2	210	220	0.0	0.0
+ch2	220	230	0.0	0.0
+ch2	230	240	0.0	0.0
+ch2	240	250	0.0	0.0
+ch2	250	260	0.0	0.0
+ch2	260	270	0.0	0.0
+ch2	270	280	0.0	0.0
+ch2	280	290	0.0	0.0
+ch2	290	300	0.0	0.0
+ch2	300	310	0.0	0.0
+ch2	310	320	0.0	0.0
+ch2	320	330	0.0	0.0
+ch2	330	340	0.0	0.0
+ch2	340	350	0.0	0.0
+ch2	350	360	0.0	0.0
+ch2	360	370	0.0	0.0
+ch2	370	380	0.0	0.0
+ch2	380	390	0.0	0.0
+ch2	390	400	0.0	0.0
+ch3	0	10	0.0	0.0
+ch3	10	20	0.0	0.0
+ch3	20	30	0.0	0.0
+ch3	30	40	0.0	0.0
+ch3	40	50	0.0	0.0
+ch3	50	60	3.0	3.0
+ch3	60	70	3.0	3.0
+ch3	70	80	1.5	1.5
+ch3	80	90	0.0	0.0
+ch3	90	100	0.0	0.0
+ch3	100	110	0.0	0.0
+ch3	110	120	0.0	0.0
+ch3	120	130	0.0	0.0
+ch3	130	140	0.0	0.0
+ch3	140	150	0.0	0.0
+ch3	150	160	1.0	1.0
+ch3	160	170	1.0	1.0
+ch3	170	180	0.5	0.5
+ch3	180	190	0.0	0.0
+ch3	190	200	0.0	0.0
+ch3	200	210	0.0	0.0
+ch3	210	220	0.0	0.0
+ch3	220	230	0.0	0.0
+ch3	230	240	0.0	0.0
+ch3	240	250	0.0	0.0
+ch3	250	260	0.0	0.0
+ch3	260	270	0.0	0.0
+ch3	270	280	0.0	0.0
+ch3	280	290	0.0	0.0
+ch3	290	300	0.0	0.0
+ch3	300	310	0.0	0.0
+ch3	310	320	0.0	0.0
+ch3	320	330	0.0	0.0
+ch3	330	340	0.0	0.0
+ch3	340	350	0.0	0.0
+ch3	350	360	0.0	0.0
+ch3	360	370	0.0	0.0
+ch3	370	380	0.0	0.0
+ch3	380	390	0.0	0.0
+ch3	390	400	0.0	0.0
Binary file test-data/test_compated.bw has changed
Binary file test-data/test_half.bw has changed