# HG changeset patch
# User pjbriggs
# Date 1687851427 0
# Node ID c7646ff9b5c95baf247154314998ed2a72438ca2
# Parent  dfb9390159355434fd7d57c19484d88ff9101feb
planemo upload commit a2f39c10087e77bde5b5db5d04305f72b8eb2af2

diff -r dfb939015935 -r c7646ff9b5c9 README.rst
--- a/README.rst	Wed Dec 12 07:55:16 2018 -0500
+++ b/README.rst	Tue Jun 27 07:37:07 2023 +0000
@@ -56,21 +56,22 @@
 to re-implement the internal workings of the tool to conform with current
 practices in invoking commands from Galaxy, and to add new functionality.
 
-========== ======================================================================
-Version    Changes
----------- ----------------------------------------------------------------------
-2.1.2.0    - Update to use MACS 2.1.2
-2.1.1.0    - Update to use MACS 2.1.1 and use conda to resolve dependencies
-2.1.0-6    - Add bedSort step into bigWig file generation; terminate with error
-             when MACS finishes with non-zero exit code.
-2.1.0-5    - User must explicitly specify the format for the inputs (to allow
-             for paired-end data)
-2.1.0-4    - Remove 'bdgcmp' functionality.
-2.1.0-3    - Add tool tests
-2.1.0-2    - Add option to create bigWig file from bedGraphs; fix bug with -B
-             option; make --mfold defaults consistent.
-2.1.0-1    - Initial version
-========== ======================================================================
+============= =================================================================
+Version       Changes
+------------- -----------------------------------------------------------------
+2.1.2-galaxy1 - Update UCSC tool dependencies to version 357
+2.1.2.0       - Update to use MACS 2.1.2
+2.1.1.0       - Update to use MACS 2.1.1 and use conda to resolve dependencies
+2.1.0-6       - Add bedSort step into bigWig file generation; terminate with
+                error when MACS finishes with non-zero exit code.
+2.1.0-5       - User must explicitly specify the format for the inputs (to
+                allow for paired-end data)
+2.1.0-4       - Remove 'bdgcmp' functionality.
+2.1.0-3       - Add tool tests
+2.1.0-2       - Add option to create bigWig file from bedGraphs; fix bug with
+                ``-B`` option; make ``--mfold`` defaults consistent.
+2.1.0-1       - Initial version
+============= =================================================================
 
 
 Developers
diff -r dfb939015935 -r c7646ff9b5c9 install_tool_deps.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/install_tool_deps.sh	Tue Jun 27 07:37:07 2023 +0000
@@ -0,0 +1,30 @@
+#!/bin/bash
+#
+# Install the tool dependencies for MACS21 for testing from command line
+#
+# Installer functions
+. $(dirname $0)/../../local_dependency_installers/numpy.sh
+. $(dirname $0)/../../local_dependency_installers/macs2.sh
+. $(dirname $0)/../../local_dependency_installers/ucsc_tools.sh
+#
+# Installation directory
+TOP_DIR=$1
+if [ -z "$TOP_DIR" ] ; then
+    echo Usage: $(basename $0) DIR
+    exit
+fi
+if [ -z "$(echo $TOP_DIR | grep ^/)" ] ; then
+    TOP_DIR=$(pwd)/$TOP_DIR
+fi
+if [ ! -d "$TOP_DIR" ] ; then
+    mkdir -p $TOP_DIR
+fi
+# Numpy 1.9
+install_numpy_1_9 $TOP_DIR
+# MACS21
+. $TOP_DIR/numpy/1.9/env.sh # needs Numpy 1.9
+install_macs2_2_1_0_20140616 $TOP_DIR
+# UCSC tool subset
+install_ucsc_tools_for_macs21_2_0 $TOP_DIR
+##
+#
diff -r dfb939015935 -r c7646ff9b5c9 macs21_wrapper.xml
--- a/macs21_wrapper.xml	Wed Dec 12 07:55:16 2018 -0500
+++ b/macs21_wrapper.xml	Tue Jun 27 07:37:07 2023 +0000
@@ -1,13 +1,13 @@
-<tool id="macs2_1_peakcalling" name="MACS2.1.2" version="2.1.2.0">
+<tool id="macs2_1_peakcalling" name="MACS2.1.2" version="2.1.2-galaxy1">
   <description>Model-based Analysis of ChIP-Seq: peak calling</description>
   <requirements>
     <requirement type="package" version="2.7">python</requirement>
     <requirement type="package" version="2.1.2">macs2</requirement>
     <requirement type="package" version="3.5">R</requirement>
-    <requirement type="package" version="357">ucsc-fetchchromsizes</requirement>
-    <requirement type="package" version="357">ucsc-bedclip</requirement>
-    <requirement type="package" version="357">ucsc-bedsort</requirement>
-    <requirement type="package" version="357">ucsc-bedgraphtobigwig</requirement>
+    <requirement type="package" version="377">ucsc-fetchchromsizes</requirement>
+    <requirement type="package" version="377">ucsc-bedclip</requirement>
+    <requirement type="package" version="377">ucsc-bedsort</requirement>
+    <requirement type="package" version="377">ucsc-bedgraphtobigwig</requirement>
   </requirements>
   <version_command>macs2 --version</version_command>
   <command><![CDATA[
diff -r dfb939015935 -r c7646ff9b5c9 package_macs21_wrapper.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/package_macs21_wrapper.sh	Tue Jun 27 07:37:07 2023 +0000
@@ -0,0 +1,24 @@
+#!/bin/sh
+#
+# Package MACS 2.1 files into tgz file for upload to
+# Galaxy toolshed
+#
+VERSION=$(grep "^<tool" macs21_wrapper.xml | grep -o -e version=\".*\" | cut -d= -f2 | tr -d \")
+TGZ=macs21-${VERSION}.tgz
+if [ -f $TGZ ] ; then
+    echo $TGZ: already exists, please remove >&2
+    exit 1
+fi
+tar cvzf $TGZ \
+    README.rst \
+    macs21_wrapper.xml \
+    macs21_wrapper.py \
+    test-data
+if [ -f $TGZ ] ; then
+    echo Created $TGZ
+else
+    echo Failed to created $TGZ >&2
+    exit 1
+fi
+##
+#
diff -r dfb939015935 -r c7646ff9b5c9 run_planemo_tests.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/run_planemo_tests.sh	Tue Jun 27 07:37:07 2023 +0000
@@ -0,0 +1,18 @@
+#!/bin/bash
+#
+# Install dependencies and set up environment for
+# the macs21 tool, then run tests using planemo
+#
+# Note that any arguments supplied to the script are
+# passed directly to the "planemo test..." invocation
+#
+# e.g. --install_galaxy (to get planemo to create a
+#                        Galaxy instance to run tests)
+#
+#      --galaxy_root DIR (to run tests using existing
+#                         Galaxy instance)
+#
+# Run the planemo tests
+planemo test $@ $(dirname $0)/macs21_wrapper.xml
+##
+#
diff -r dfb939015935 -r c7646ff9b5c9 test-data/test_MACS2.1.1_peaks.xls.re_match~
--- a/test-data/test_MACS2.1.1_peaks.xls.re_match~	Wed Dec 12 07:55:16 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
-\#peaks\ file
-\#\ This\ file\ is\ generated\ by\ MACS\ version\ 2\.1\.1\.20160309
-\#\ Command\ line\:\ callpeak\ \-t\ \/tmp\/tmpHxmla3\/files\/000\/dataset\_9\.dat\ \-c\ \/tmp\/tmpHxmla3\/files\/000\/dataset\_10\.dat\ \-\-format\=BED\ \-\-name\=test\_MACS2\.1\.1\ \-\-bw\=300\ \-\-gsize\=775000000\.0\ \-\-nomodel\ \-\-extsize\=243\ \-\-qvalue\=0\.05\ \-B\ \-\-SPMR\ \-\-mfold\ 5\ 50\ \-\-keep\-dup\ 1
-\#\ ARGUMENTS\ LIST\:
-\#\ name\ \=\ test\_MACS2\.1\.1
-\#\ format\ \=\ BED
-\#\ ChIP\-seq\ file\ \=\ \[\'\/tmp\/tmpHxmla3\/files\/000\/dataset\_9\.dat\'\]
-\#\ control\ file\ \=\ \[\'\/tmp\/tmpHxmla3\/files\/000\/dataset\_10\.dat\'\]
-\#\ effective\ genome\ size\ \=\ 7\.75e\+08
-\#\ band\ width\ \=\ 300
-\#\ model\ fold\ \=\ \[5\,\ 50\]
-\#\ qvalue\ cutoff\ \=\ 5\.00e\-02
-\#\ Larger\ dataset\ will\ be\ scaled\ towards\ smaller\ dataset\.
-\#\ Range\ for\ calculating\ regional\ lambda\ is\:\ 1000\ bps\ and\ 10000\ bps
-\#\ Broad\ region\ calling\ is\ off
-\#\ Paired\-End\ mode\ is\ off
-\#\ MACS\ will\ save\ fragment\ pileup\ signal\ per\ million\ reads
-
-\#\ tag\ size\ is\ determined\ as\ 50\ bps
-\#\ total\ tags\ in\ treatment\:\ 50
-\#\ tags\ after\ filtering\ in\ treatment\:\ 50
-\#\ maximum\ duplicate\ tags\ at\ the\ same\ position\ in\ treatment\ \=\ 1
-\#\ Redundant\ rate\ in\ treatment\:\ 0\.00
-\#\ total\ tags\ in\ control\:\ 50
-\#\ tags\ after\ filtering\ in\ control\:\ 50
-\#\ maximum\ duplicate\ tags\ at\ the\ same\ position\ in\ control\ \=\ 1
-\#\ Redundant\ rate\ in\ control\:\ 0\.00
-\#\ d\ \=\ 243
-\#chr\	start\	end\	length\	abs\_summit\	pileup\	\-log10\(pvalue\)\	fold\_enrichment\	\-log10\(qvalue\)\	name
-chr26\	4118914\	4119282\	369\	4119130\	9\.00\	9\.13132\	6\.31632\	2\.51561\	test\_MACS2\.1\.1\_peak\_1