Mercurial > repos > pjbriggs > macs21
changeset 17:f346287fe52c draft
Uploaded
author | pjbriggs |
---|---|
date | Tue, 26 Jul 2016 09:54:21 -0400 |
parents | 062311890289 |
children | 4e85d68a2347 |
files | README.rst macs21_wrapper.xml tool_dependencies.xml |
diffstat | 3 files changed, 18 insertions(+), 13 deletions(-) [+] |
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--- a/README.rst Mon Jun 15 08:32:55 2015 -0400 +++ b/README.rst Tue Jul 26 09:54:21 2016 -0400 @@ -59,6 +59,8 @@ ========== ====================================================================== Version Changes ---------- ---------------------------------------------------------------------- +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
--- a/macs21_wrapper.xml Mon Jun 15 08:32:55 2015 -0400 +++ b/macs21_wrapper.xml Tue Jul 26 09:54:21 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="macs2_1_peakcalling" name="MACS2.1.0" version="2.1.0-4"> +<tool id="macs2_1_peakcalling" name="MACS2.1.0" version="2.1.0-5"> <description>Model-based Analysis of ChIP-Seq: peak calling</description> <requirements> <requirement type="package" version="2.7">python</requirement> @@ -19,7 +19,7 @@ -c $input_control_file1 #end if ## - --format=$input_chipseq_file1.extension + --format=$format --name="$experiment_name" --bw=$bw ## @@ -114,6 +114,15 @@ value="0.1" help="default: 0.1 (--broad-cutoff)"/> </when> </conditional> + <param name="format" type="select" label="Format of input read data" + help="Specify the format of the input data and whether or not it is paired end (--format)"> + <option value="BAMPE" selected="true">BAM (paired-end)</option> + <option value="BAM">BAM (single-end)</option> + <option value="BEDPE">BED (paired-end)</option> + <option value="BED">BED (single-end)</option> + <option value="SAMPE">SAM (paired-end)</option> + <option value="SAM">SAM (single-end)</option> + </param> <param name="input_chipseq_file1" type="data" format="bed,sam,bam" label="ChIP-seq read file" /> <param name="input_control_file1" type="data" format="bed,sam,bam" optional="True" @@ -270,6 +279,7 @@ <!-- Inputs --> <param name="experiment_name" value="test_MACS2.1.0" /> <param name="broad_regions" value="" /> + <param name="format" value="BED" /> <param name="input_chipseq_file1" value="test_region_IP.bed" dbkey="galGal3" ftype="bed" /> <param name="input_control_file1" value="test_region_Input.bed" @@ -308,6 +318,7 @@ <!-- Inputs --> <param name="experiment_name" value="test_MACS2.1.0" /> <param name="broad_regions" value="" /> + <param name="format" value="BED" /> <param name="input_chipseq_file1" value="test_region_IP.bed" dbkey="galGal3" ftype="bed" /> <param name="input_control_file1" value="test_region_Input.bed"
--- a/tool_dependencies.xml Mon Jun 15 08:32:55 2015 -0400 +++ b/tool_dependencies.xml Tue Jul 26 09:54:21 2016 -0400 @@ -2,10 +2,10 @@ <tool_dependency> <!-- Dependencies from main/test toolsheds --> <package name="numpy" version="1.9"> - <repository changeset_revision="43cb426cb05d" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="1e2b7e63dec2" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="R" version="3.1.2"> - <repository changeset_revision="41f43a2064ba" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="1ca39eb16186" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <!-- Subset of UCSC tools --> <package name="ucsc_tools_for_macs21" version="1.0"> @@ -45,20 +45,12 @@ <action type="download_by_url">https://pypi.python.org/packages/source/M/MACS2/MACS2-2.1.0.20140616.tar.gz</action> <!-- Install environment for main & test toolsheds --> <action type="set_environment_for_install"> - <repository changeset_revision="43cb426cb05d" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <repository changeset_revision="1e2b7e63dec2" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> <package name="numpy" version="1.9" /> </repository> - <repository changeset_revision="4778b172b895" name="package_atlas_3_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="atlas" version="3.10.2" /> - </repository> </action> <action type="make_directory">$INSTALL_DIR/lib/python</action> <action type="shell_command"> - echo PWD is: ; - pwd ; - echo PYTHONPATH is $PYTHONPATH ; - python -c "import numpy" ; - echo About to do the operations: ; export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin </action>