| Previous changeset 4:384b972e43bc (2017-08-01) Next changeset 6:7e47f78590cc (2017-09-15) |
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Commit message:
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6 |
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modified:
je-markdupes.xml macros.xml |
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removed:
je je_1.2_bundle.jar |
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| diff -r 384b972e43bc -r e2d1b5e1eb11 je --- a/je Tue Aug 01 03:43:03 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,18 +0,0 @@ -#!/bin/sh -# Wrapper around je_1.1_bundle.jar - -# where are we stored ? -DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" -# echo $DIR -# path to jar file to execute, this jar is supposed to be in the same dir as this script -JAR_FILE=$DIR"/je_1.2_bundle.jar" - -# set default _JAVA_OPTIONS -_JAVA_OPTIONS=${_JAVA_OPTIONS:-'-Xmx4G -Xms256m'} -export _JAVA_OPTIONS - -# uncomment to change logging level using your own log4j.xml found in $DIR file -# OPTS="-Dlog4j.configuration=file:$DIR/log4j.xml" - -java $OPTS -jar $JAR_FILE "$@" -exit $? |
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| diff -r 384b972e43bc -r e2d1b5e1eb11 je-markdupes.xml --- a/je-markdupes.xml Tue Aug 01 03:43:03 2017 -0400 +++ b/je-markdupes.xml Wed Aug 02 10:59:49 2017 -0400 |
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| @@ -3,11 +3,12 @@ <macros> <import>macros.xml</import> </macros> + <expand macro="requirements" /> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> </stdio> - <version_command>echo '1.0'</version_command> - <command interpreter="bash"> + <expand macro="version_command" /> + <command> <![CDATA[ je markdupes @@ -182,8 +183,7 @@ </test> </tests> - - <help> + <help> <![CDATA[ **What it does** @@ -403,6 +403,6 @@ to clear the default value. ]]> - </help> - + </help> + <expand macro="citations"/> </tool> |
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| diff -r 384b972e43bc -r e2d1b5e1eb11 je_1.2_bundle.jar |
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| Binary file je_1.2_bundle.jar has changed |
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| diff -r 384b972e43bc -r e2d1b5e1eb11 macros.xml --- a/macros.xml Tue Aug 01 03:43:03 2017 -0400 +++ b/macros.xml Wed Aug 02 10:59:49 2017 -0400 |
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| @@ -1,6 +1,14 @@ <macros> <token name="@VERSION_STRING@">1.2</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.2">je-suite</requirement> + </requirements> + </xml> + <xml name="version_command"> + <version_command>je version 2>&1 | tail -n 1</version_command> + </xml> <token name="@single_or_paired_cmd@"> #if str( $library.type ) == "single": @@ -278,7 +286,7 @@ </token> <xml name="demultiplexer_common_output_options"> <param name="KEEP_UNASSIGNED_READ" type="boolean" label="Keep unassigned reads (KEEP_UNASSIGNED_READ)" - truealue="true" + truevalue="true" falsevalue="false" checked="true" /> @@ -317,11 +325,9 @@ help="Set to empty or null for no replacement." value=":"/> - <param name="GZ" type="boolean" hidden="true" label="Compress output (GZ)" + <param name="GZ" type="hidden" label="Compress output (GZ)" help="will result in fastq.gz files." - truevalue="true" - falsevalue="false" - checked="false"/> + value="false"/> </xml> <token name="@demultiplexer_common_outputs_cmd@"> @@ -336,5 +342,9 @@ <filter>(adv_options['DIAG'] == 'true')</filter> </data> </xml> - + <xml name="citations"> + <citations> + <citation type="doi">10.1186/s12859-016-1284-2</citation> + </citations> + </xml> </macros> |