Mercurial > repos > refinery-platform > picard_merge_sam_files
changeset 8:afcccc536c1d draft default tip
planemo upload for repository https://github.com/scottx611x/picard_MergeSamFiles commit 18b5e06ecfca32bbeed3306c4576ddb500d71cc1
| author | refinery-platform |
|---|---|
| date | Mon, 24 Sep 2018 10:51:56 -0400 |
| parents | 28f273969b5e |
| children | |
| files | picard_MergeSamFiles.xml picard_macros.xml tool_dependencies.xml |
| diffstat | 3 files changed, 9 insertions(+), 27 deletions(-) [+] |
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--- a/picard_MergeSamFiles.xml Mon Dec 04 10:52:59 2017 -0500 +++ b/picard_MergeSamFiles.xml Mon Sep 24 10:51:56 2018 -0400 @@ -1,17 +1,14 @@ <tool name="MergeSamFiles" id="picard_MergeSamFiles" version="@TOOL_VERSION@.0"> <description>merges multiple SAM/BAM datasets into one</description> - <requirements> - <requirement type="package" version="1.126.0">picard</requirement> - </requirements> - <macros> <import>picard_macros.xml</import> </macros> + <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @java_options@ #for $index, $listCollection in enumerate($inputList): && - java -jar \$JAVA_JAR_PATH/picard.jar + picard MergeSamFiles #for $element in $listCollection:
--- a/picard_macros.xml Mon Dec 04 10:52:59 2017 -0500 +++ b/picard_macros.xml Mon Sep 24 10:51:56 2018 -0400 @@ -9,6 +9,13 @@ <token name="@TOOL_VERSION@">2.7.1</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.7.1">picard</requirement> + <yield/> + </requirements> + </xml> + <token name="@symlink_element_identifier@"><![CDATA[ #import re #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
--- a/tool_dependencies.xml Mon Dec 04 10:52:59 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="picard" version="1.126.0"> - <install version="1.0"> - <actions_group> - <actions architecture="x86_64" os="linux"> - <action type="download_by_url">https://github.com/broadinstitute/picard/releases/download/1.126/picard-tools-1.126.zip</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> - </actions> - <action type="set_environment"> - <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable> - </action> - </actions_group> - </install> - <readme> -This picard package dependency is retrieved directly from https://github.com/broadinstitute/picard/releases - </readme> - </package> -</tool_dependency> \ No newline at end of file