Commit 0eefd837 authored by Jelle Scholtalbers's avatar Jelle Scholtalbers 🇳🇱

use conda package for galaxy wrapper

parent 9bdeeacb
#!/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 $?
...@@ -3,11 +3,12 @@ ...@@ -3,11 +3,12 @@
<macros> <macros>
<import>macros.xml</import> <import>macros.xml</import>
</macros> </macros>
<expand macro="requirements" />
<stdio> <stdio>
<exit_code range="1:" level="fatal" description="Tool exception" /> <exit_code range="1:" level="fatal" description="Tool exception" />
</stdio> </stdio>
<version_command>echo '1.0'</version_command> <expand macro="version_command" />
<command interpreter="bash"> <command>
<![CDATA[ <![CDATA[
je clip je clip
...@@ -85,8 +86,7 @@ ...@@ -85,8 +86,7 @@
</test> </test>
</tests> </tests>
<help>
<help>
<![CDATA[ <![CDATA[
**What it does** **What it does**
...@@ -242,6 +242,6 @@ This is an exhaustive list of options:: ...@@ -242,6 +242,6 @@ This is an exhaustive list of options::
Default value: null. Default value: null.
]]> ]]>
</help> </help>
<expand macro="citations"/>
</tool> </tool>
...@@ -3,11 +3,12 @@ ...@@ -3,11 +3,12 @@
<macros> <macros>
<import>macros.xml</import> <import>macros.xml</import>
</macros> </macros>
<expand macro="requirements" />
<stdio> <stdio>
<exit_code range="1:" level="fatal" description="Tool exception" /> <exit_code range="1:" level="fatal" description="Tool exception" />
</stdio> </stdio>
<version_command>echo '1.0'</version_command> <expand macro="version_command" />
<command interpreter="bash"> <command>
<![CDATA[ <![CDATA[
je demultiplex-illu je demultiplex-illu
...@@ -93,7 +94,7 @@ ...@@ -93,7 +94,7 @@
<param name="MM" value="3"/> <param name="MM" value="3"/>
<param name="MMD" value="2"/> <param name="MMD" value="2"/>
<param name="Q" value="20"/> <param name="Q" value="20"/>
<param name="DIAG" value="false"/> <param name="DIAG" value="false"/>
<output name="METRICS_FILE_NAME" file="illu_summary_PE.txt" ftype="tabular" lines_diff="4"> <output name="METRICS_FILE_NAME" file="illu_summary_PE.txt" ftype="tabular" lines_diff="4">
<discovered_dataset designation="unassigned_1" file="illu_unassigned_1_PE.txt" /> <discovered_dataset designation="unassigned_1" file="illu_unassigned_1_PE.txt" />
<discovered_dataset designation="unassigned_2" file="illu_unassigned_2_PE.txt" /> <discovered_dataset designation="unassigned_2" file="illu_unassigned_2_PE.txt" />
...@@ -111,8 +112,7 @@ ...@@ -111,8 +112,7 @@
</test> </test>
</tests> </tests>
<help>
<help>
<![CDATA[ <![CDATA[
**What it does** **What it does**
...@@ -423,6 +423,6 @@ This is an exhaustive list of options:: ...@@ -423,6 +423,6 @@ This is an exhaustive list of options::
Default value: null. Default value: null.
]]> ]]>
</help> </help>
<expand macro="citations"/>
</tool> </tool>
...@@ -3,11 +3,12 @@ ...@@ -3,11 +3,12 @@
<macros> <macros>
<import>macros.xml</import> <import>macros.xml</import>
</macros> </macros>
<expand macro="requirements" />
<stdio> <stdio>
<exit_code range="1:" level="fatal" description="Tool exception" /> <exit_code range="1:" level="fatal" description="Tool exception" />
</stdio> </stdio>
<version_command>echo '1.0'</version_command> <expand macro="version_command" />
<command interpreter="bash"> <command>
<![CDATA[ <![CDATA[
je demultiplex je demultiplex
...@@ -91,8 +92,7 @@ ...@@ -91,8 +92,7 @@
</test> </test>
</tests> </tests>
<help>
<help>
<![CDATA[ <![CDATA[
**What it does** **What it does**
...@@ -434,6 +434,6 @@ This is an exhaustive list of options:: ...@@ -434,6 +434,6 @@ This is an exhaustive list of options::
Default value: null. Default value: null.
]]> ]]>
</help> </help>
<expand macro="citations"/>
</tool> </tool>
...@@ -3,11 +3,12 @@ ...@@ -3,11 +3,12 @@
<macros> <macros>
<import>macros.xml</import> <import>macros.xml</import>
</macros> </macros>
<expand macro="requirements" />
<stdio> <stdio>
<exit_code range="1:" level="fatal" description="Tool exception" /> <exit_code range="1:" level="fatal" description="Tool exception" />
</stdio> </stdio>
<version_command>echo '1.0'</version_command> <expand macro="version_command" />
<command interpreter="bash"> <command>
<![CDATA[ <![CDATA[
je markdupes je markdupes
...@@ -182,8 +183,7 @@ ...@@ -182,8 +183,7 @@
</test> </test>
</tests> </tests>
<help>
<help>
<![CDATA[ <![CDATA[
**What it does** **What it does**
...@@ -403,6 +403,6 @@ This is an exhaustive list of options:: ...@@ -403,6 +403,6 @@ This is an exhaustive list of options::
to clear the default value. to clear the default value.
]]> ]]>
</help> </help>
<expand macro="citations"/>
</tool> </tool>
<macros> <macros>
<token name="@VERSION_STRING@">1.2</token> <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&gt;&amp;1 | tail -n 1</version_command>
</xml>
<token name="@single_or_paired_cmd@"> <token name="@single_or_paired_cmd@">
#if str( $library.type ) == "single": #if str( $library.type ) == "single":
...@@ -278,7 +286,7 @@ ${from_text_area}</configfile> ...@@ -278,7 +286,7 @@ ${from_text_area}</configfile>
</token> </token>
<xml name="demultiplexer_common_output_options"> <xml name="demultiplexer_common_output_options">
<param name="KEEP_UNASSIGNED_READ" type="boolean" label="Keep unassigned reads (KEEP_UNASSIGNED_READ)" <param name="KEEP_UNASSIGNED_READ" type="boolean" label="Keep unassigned reads (KEEP_UNASSIGNED_READ)"
truealue="true" truevalue="true"
falsevalue="false" falsevalue="false"
checked="true" checked="true"
/> />
...@@ -317,11 +325,9 @@ ${from_text_area}</configfile> ...@@ -317,11 +325,9 @@ ${from_text_area}</configfile>
help="Set to empty or null for no replacement." help="Set to empty or null for no replacement."
value=":"/> 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." help="will result in fastq.gz files."
truevalue="true" value="false"/>
falsevalue="false"
checked="false"/>
</xml> </xml>
<token name="@demultiplexer_common_outputs_cmd@"> <token name="@demultiplexer_common_outputs_cmd@">
...@@ -336,5 +342,9 @@ ${from_text_area}</configfile> ...@@ -336,5 +342,9 @@ ${from_text_area}</configfile>
<filter>(adv_options['DIAG'] == 'true')</filter> <filter>(adv_options['DIAG'] == 'true')</filter>
</data> </data>
</xml> </xml>
<xml name="citations">
<citations>
<citation type="doi">10.1186/s12859-016-1284-2</citation>
</citations>
</xml>
</macros> </macros>
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