| Previous changeset 0:7e55ac3bd458 (2015-06-09) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/ commit 608bf2d6f11fe6dceaa0060f729bdbb66cfee867 |
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modified:
compalignp.xml |
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removed:
tool_dependencies.xml |
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| diff -r 7e55ac3bd458 -r f3a318881b1b compalignp.xml --- a/compalignp.xml Tue Jun 09 05:36:03 2015 -0400 +++ b/compalignp.xml Sun Nov 12 06:10:42 2017 -0500 |
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| @@ -3,21 +3,17 @@ <requirements> <requirement type="package" version="1.0">compalignp</requirement> </requirements> - <stdio> - <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" /> - <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" /> - </stdio> - <command> + <command detect_errors="aggressive"> <![CDATA[ compalignp - -t $rna_alignment_target - -r $rna_alignment_reference + -t '$rna_alignment_target' + -r '$rna_alignment_reference' > $output ]]> </command> <inputs> - <param format="clustalw,stockholm" name="rna_alignment_target" type="data" label="Target RNA Alignment" help="(-t)" /> - <param format="clustalw,stockholm" name="rna_alignment_reference" type="data" label="Reference RNA Alignment" help="(-r)" /> + <param format="clustal,stockholm" name="rna_alignment_target" type="data" label="Target RNA Alignment" help="(-t)" /> + <param format="clustal,stockholm" name="rna_alignment_reference" type="data" label="Reference RNA Alignment" help="(-r)" /> </inputs> <outputs> <data name="output" format="txt" /> @@ -31,6 +27,7 @@ </tests> <help> <![CDATA[ + **compalignp** > Paranoia version of squids compalign. @@ -43,6 +40,6 @@ ]]> </help> <citations> - <citation type="doi">10.1186/1748-7188-1-19</citation> + <citation type="doi">10.1186/1748-7188-1-19</citation> </citations> </tool> |
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| diff -r 7e55ac3bd458 -r f3a318881b1b tool_dependencies.xml --- a/tool_dependencies.xml Tue Jun 09 05:36:03 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,27 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="squid" version="1.9g"> - <repository changeset_revision="a82a68a3374e" name="package_squid_1_9g" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="compalignp" version="1.0"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://www.biophys.uni-duesseldorf.de/bralibase/compalignp.tgz</action> - <action type="set_environment_for_install"> - <repository changeset_revision="a82a68a3374e" name="package_squid_1_9g" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> - <package name="squid" version="1.9g" /> - </repository> - </action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>compalignp</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - <environment_variable action="set_to" name="COMPALIGNP_ROOT_PATH">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - </package> -</tool_dependency> |