| Previous changeset 0:06cb587a5e87 (2015-06-30) Next changeset 2:00d73c812399 (2017-03-22) |
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Commit message:
Uploaded latest version 2.1.0-5. |
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modified:
README.rst macs21_wrapper.xml tool_dependencies.xml |
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| diff -r 06cb587a5e87 -r 02a01ea54722 README.rst --- a/README.rst Tue Jun 30 08:16:18 2015 -0400 +++ b/README.rst Tue Jul 26 10:34:49 2016 -0400 |
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| @@ -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 |
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| diff -r 06cb587a5e87 -r 02a01ea54722 macs21_wrapper.xml --- a/macs21_wrapper.xml Tue Jun 30 08:16:18 2015 -0400 +++ b/macs21_wrapper.xml Tue Jul 26 10:34:49 2016 -0400 |
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| @@ -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" |
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| diff -r 06cb587a5e87 -r 02a01ea54722 tool_dependencies.xml --- a/tool_dependencies.xml Tue Jun 30 08:16:18 2015 -0400 +++ b/tool_dependencies.xml Tue Jul 26 10:34:49 2016 -0400 |
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| @@ -2,10 +2,10 @@ <tool_dependency> <!-- Dependencies from main/test toolsheds --> <package name="numpy" version="1.9"> - <repository changeset_revision="84e97f5cd3ab" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="83d12e13dbbd" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="R" version="3.1.2"> - <repository changeset_revision="6e0eee4ea4e1" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <!-- Subset of UCSC tools --> <package name="ucsc_tools_for_macs21" version="1.0"> @@ -45,7 +45,7 @@ <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="84e97f5cd3ab" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <repository changeset_revision="83d12e13dbbd" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> <package name="numpy" version="1.9" /> </repository> </action> |