Commit 58a5df4f authored by Jelle Scholtalbers's avatar Jelle Scholtalbers

galaxy wrapper updates

parent 8989f33b
#!/bin/sh
# Wrapper around je_1.0_bundle.jar
#where are we stored ?
# 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
# 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_1.0_bundle.jar"
OPTS="-Xmx2g"
#uncomment to change logging level using your own log4j.xml found in $DIR file
OPTS=$OPTS" -Dlog4j.configuration=file:$DIR/log4j.xml"
# uncomment to change logging level using your own log4j.xml found in $DIR file
# OPTS=$OPTS" -Dlog4j.configuration=file:$DIR/log4j.xml"
java $OPTS -jar $JAR_FILE "$@"
exit $?
\ No newline at end of file
exit $?
#!/bin/sh
# Wrapper around je_embl_1.0_bundle.jar
#path to jar file to execute
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
#echo $DIR
JAR_FILE=$DIR"/je_1.0_bundle.jar"
OPTS="-Xmx8g"
java $OPTS -jar $JAR_FILE "$@"
exit $?
../../dist/je
\ No newline at end of file
......@@ -89,7 +89,7 @@
**What it does**
Je clip: Clips barcodes or Unique Molecular Identifiers (UMIs) from the input fastq files
Input files are fastq files, and can be in gzip compressed format (end in .gz).
Input files are fastq files, and can be in gzip compressed format.
Author: Charles Girardot (charles.girardot@embl.de).
......@@ -101,7 +101,7 @@ Wrapper by: Jelle Scholtalbers (jelle.scholtalbers@embl.de).
.. class:: warningmark
You will want to read the `documentation`__.
You will want to read the `documentation`__.
.. __: http://gbcs.embl.de/portal/Je
......
......@@ -93,8 +93,8 @@
<param name="MM" value="3"/>
<param name="MMD" value="2"/>
<param name="Q" value="20"/>
<output name="METRICS_FILE_NAME" file="illu_summary_PE.txt" ftype="tabular">
<param name="DIAG" value="false"/>
<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_2" file="illu_unassigned_2_PE.txt" />
<discovered_dataset designation="emb681m5_GGACTCCTCTCTCTAT_2" file="emb681m5_GGACTCCTCTCTCTAT_2.txt"/>
......@@ -118,7 +118,7 @@
Je demultiplex-illu: demultiplex fastq files using Illumina Index files,
with optional handling of Unique Molecular Identifiers for further use in 'markdupes' module
Input files are fastq files, and can be in gzip compressed format (end in .gz).
Input files are fastq files, and can be in gzip compressed format.
Author: Charles Girardot (charles.girardot@embl.de).
......@@ -130,7 +130,7 @@ Wrapper by: Jelle Scholtalbers (jelle.scholtalbers@embl.de).
.. class:: warningmark
You will want to read the `documentation`__.
You will want to read the `documentation`__.
.. __: http://gbcs.embl.de/portal/Je
......
......@@ -59,7 +59,7 @@
<param name="type" value="single"/>
<param name="input_1" value="file_1_sequence.txt" ftype="fastqsanger"/>
<param name="BARCODE_FILE" value="barcodes_SE.txt" ftype="tabular"/>
<output name="METRICS_FILE_NAME" file="summary_SE.txt" ftype="tabular">
<output name="METRICS_FILE_NAME" file="summary_SE.txt" ftype="tabular" lines_diff="4">
<discovered_dataset designation="unassigned_1" file="unassigned_1_SE.txt" />
</output>
</test>
......@@ -76,7 +76,7 @@
<param name="barcode_list_type_con" value="text"/>
<param name="barcode_text"
value="sample1 CACTGT:GTATAG&#10;sample2 ATTCCG:TCCGTC&#10;sample3 GCTACC:TGGTCA&#10;sample4 CGAAAC:CACTGT"/>
<output name="METRICS_FILE_NAME" file="summary_PE.txt" ftype="tabular">
<output name="METRICS_FILE_NAME" file="summary_PE.txt" ftype="tabular" lines_diff="4">
<discovered_dataset designation="unassigned_1" file="unassigned_1_PE.txt" />
<discovered_dataset designation="unassigned_2" file="unassigned_2_PE.txt" />
<discovered_dataset designation="sample4_CGAAACCACTGT_2" file="sample4_CGAAACCACTGT_2.txt"/>
......@@ -98,7 +98,7 @@
Je demultiplex: A fastq file demultiplexer with optional handling of Unique Molecular Identifiers for further use
in 'markdupes' module.
Input files are fastq files, and can be in gzip compressed format (end in .gz).
Input files are fastq files, and can be in gzip compressed format.
Author: Charles Girardot (charles.girardot@embl.de).
......@@ -110,7 +110,7 @@ Wrapper by: Jelle Scholtalbers (jelle.scholtalbers@embl.de).
.. class:: warningmark
You will want to read the `documentation`__.
You will want to read the `documentation`__.
.. __: http://gbcs.embl.de/portal/Je
......
......@@ -162,20 +162,6 @@
</outputs>
<tests>
<test>
<!-- picard markduplicates default test -->
<param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/>
<param name="barcode_list_type_con" value="no_barcodes"/>
<param name="comment" value="test-run"/>
<param name="assume_sorted" value="True"/>
<param name="remove_duplicates" value="True"/>
<param name="read_name_regex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*."/>
<param name="optical_duplicate_pixel_distance" value="100"/>
<param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/>
<param name="validation_stringency" value="LENIENT"/>
<!-- TODO: the diff is set too high and the test might be incorrect as je markdupes expects barcodes -->
<output name="outFile" file="picard_MarkDuplicates_test1.bam" ftype="bam" lines_diff="7"/>
</test>
<test>
<!-- picard markduplicates default test -->
<param name="inputFile" value="markdupes_DNase_sorted.bam" ftype="bam"/>
......@@ -218,7 +204,7 @@ Wrapper by: Jelle Scholtalbers (jelle.scholtalbers@embl.de).
.. class:: warningmark
You will want to read the `documentation`__.
You will want to read the `documentation`__.
.. __: http://gbcs.embl.de/portal/Je
......@@ -420,4 +406,4 @@ This is an exhaustive list of options::
]]>
</help>
</tool>
\ No newline at end of file
</tool>
../../bin/je_1.0_bundle.jar
\ No newline at end of file
../../dist/je_1.0_bundle.jar
\ No newline at end of file
......@@ -329,7 +329,7 @@ ${from_text_area}</configfile>
<discover_datasets pattern="(?P&lt;name&gt;.*)\.txt" directory="results" visible="true" ext="fastqsanger"/>
</data>
<data name="BARCODE_DIAG_FILE" format="tabular" label="Barcode statistics">
<filter>(adv_options.DIAG == 'true')</filter>
<filter>(adv_options['DIAG'] == 'true')</filter>
</data>
</xml>
......
Processed_read_pairs 25
Assigned 10
Unassigned_read_pairs 15
##
##
Processed Reads (pairs) 25
Assigned Reads (pairs) 10
Unassigned Reads (pairs) 15
# Individual sample read (pair) counts :
emb681m1 2
emb681m4 2
emb681m5 2
......
Processed_read_pairs 25
Assigned 25
Unassigned_read_pairs 0
##
##
Processed Reads (pairs) 25
Assigned Reads (pairs) 25
Unassigned Reads (pairs) 0
# Individual sample read (pair) counts :
sample1 6
sample4 6
sample3 6
......
Processed_read_pairs 25
Assigned 25
Unassigned_read_pairs 0
##
##
Processed Reads (pairs) 25
Assigned Reads (pairs) 25
Unassigned Reads (pairs) 0
# Individual sample read (pair) counts :
sample1 6
sample4 6
sample3 6
......
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