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GBCS
Je
Commits
8adb16fc
Commit
8adb16fc
authored
Mar 05, 2018
by
Jelle Scholtalbers
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Merge branch 'mtekman-master'
parents
25e8fd29
02cddee5
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3
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3 changed files
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60 additions
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17 deletions
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-17
src/galaxy/je-demultiplex-illu.xml
src/galaxy/je-demultiplex-illu.xml
+3
-1
src/galaxy/je-demultiplex.xml
src/galaxy/je-demultiplex.xml
+33
-2
src/galaxy/macros.xml
src/galaxy/macros.xml
+24
-14
No files found.
src/galaxy/je-demultiplex-illu.xml
View file @
8adb16fc
...
...
@@ -95,7 +95,8 @@
<param
name=
"MMD"
value=
"2"
/>
<param
name=
"Q"
value=
"20"
/>
<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"
/>
<output
name=
"DEMULTIPLEX_RESULTS"
ftype=
"tabular"
>
<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"
/>
...
...
@@ -123,6 +124,7 @@ Input files are fastq files, and can be in gzip compressed format.
Author: Charles Girardot (charles.girardot@embl.de).
Wrapper by: Jelle Scholtalbers (jelle.scholtalbers@embl.de).
With contributions by: Mehmet Tekman (@mtekman)
------
...
...
src/galaxy/je-demultiplex.xml
View file @
8adb16fc
...
...
@@ -60,7 +60,8 @@
<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"
lines_diff=
"4"
>
<output
name=
"METRICS_FILE_NAME"
file=
"summary_SE.txt"
ftype=
"tabular"
lines_diff=
"4"
/>
<output
name=
"DEMULTIPLEX_RESULTS"
ftype=
"tabular"
>
<discovered_dataset
designation=
"unassigned_1"
file=
"unassigned_1_SE.txt"
/>
</output>
</test>
...
...
@@ -74,10 +75,12 @@
<param
name=
"BM"
value=
"BOTH"
/>
<param
name=
"BRED"
value=
"false"
/>
<param
name=
"COLLECT_OUTPUTS"
value=
"false"
/>
<param
name=
"barcode_list_type_con"
value=
"text"
/>
<param
name=
"barcode_text"
value=
"sample1 CACTGT:GTATAG sample2 ATTCCG:TCCGTC sample3 GCTACC:TGGTCA sample4 CGAAAC:CACTGT"
/>
<output
name=
"METRICS_FILE_NAME"
file=
"summary_PE.txt"
ftype=
"tabular"
lines_diff=
"4"
>
<output
name=
"METRICS_FILE_NAME"
file=
"summary_PE.txt"
ftype=
"tabular"
lines_diff=
"4"
/>
<output
name=
"DEMULTIPLEX_RESULTS"
ftype=
"tabular"
>
<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"
/>
...
...
@@ -90,6 +93,33 @@
<discovered_dataset
designation=
"sample1_CACTGTGTATAG_1"
file=
"sample1_CACTGTGTATAG_1.txt"
/>
</output>
</test>
<test>
<!-- Repeat of previous but with collection outputs -->
<param
name=
"type"
value=
"paired"
/>
<param
name=
"input_1"
value=
"file_1_sequence.txt"
ftype=
"fastqsanger"
/>
<param
name=
"input_2"
value=
"file_2_sequence.txt"
ftype=
"fastqsanger"
/>
<param
name=
"BPOS"
value=
"BOTH"
/>
<param
name=
"BM"
value=
"BOTH"
/>
<param
name=
"BRED"
value=
"false"
/>
<param
name=
"barcode_list_type_con"
value=
"text"
/>
<param
name=
"barcode_text"
value=
"sample1 CACTGT:GTATAG sample2 ATTCCG:TCCGTC sample3 GCTACC:TGGTCA sample4 CGAAAC:CACTGT"
/>
<param
name=
"COLLECT_OUTPUTS"
value=
"true"
/>
<output_collection
name=
"COLLECTION_1"
type=
"list"
>
<element
name=
"sample1_CACTGTGTATAG_1.txt"
value=
"sample4_CGAAACCACTGT_1.txt"
/>
<element
name=
"sample3_GCTACCTGGTCA_1.txt"
value=
"sample3_GCTACCTGGTCA_1.txt"
/>
<element
name=
"sample2_ATTCCGTCCGTC_1.txt"
value=
"sample2_ATTCCGTCCGTC_1.txt"
/>
<element
name=
"sample1_CACTGTGTATAG_1.txt"
value=
"sample1_CACTGTGTATAG_1.txt"
/>
</output_collection>
<output_collection
name=
"COLLECTION_2"
type=
"list"
>
<element
name=
"sample4_CGAAACCACTGT_2.txt"
value=
"sample4_CGAAACCACTGT_2.txt"
/>
<element
name=
"sample3_GCTACCTGGTCA_2.txt"
value=
"sample3_GCTACCTGGTCA_2.txt"
/>
<element
name=
"sample2_ATTCCGTCCGTC_2.txt"
value=
"sample2_ATTCCGTCCGTC_2.txt"
/>
<element
name=
"sample1_CACTGTGTATAG_2.txt"
value=
"sample1_CACTGTGTATAG_2.txt"
/>
</output_collection>
</test>
</tests>
<help>
...
...
@@ -103,6 +133,7 @@ Input files are fastq files, and can be in gzip compressed format.
Author: Charles Girardot (charles.girardot@embl.de).
Wrapper by: Jelle Scholtalbers (jelle.scholtalbers@embl.de).
With contributions by: Mehmet Tekman (@mtekman)
------
...
...
src/galaxy/macros.xml
View file @
8adb16fc
<macros>
<token
name=
"@VERSION_STRING@"
>
1.2
</token>
<token
name=
"@VERSION_STRING@"
>
1.2
.1
</token>
<xml
name=
"requirements"
>
<requirements>
<requirement
type=
"package"
version=
"1.2"
>
je-suite
</requirement>
...
...
@@ -278,19 +278,19 @@ ${from_text_area}</configfile>
</xml>
<token
name=
"@demultiplexer_common_output_options_cmd@"
>
KEEP_UNASSIGNED_READ=$KEEP_UNASSIGNED_READ
STATS_ONLY=${
adv_options.
STATS_ONLY}
#if str( $
adv_options.
DIAG ) == "true":
KEEP_UNASSIGNED_READ=$
{
KEEP_UNASSIGNED_READ
}
STATS_ONLY=${STATS_ONLY}
#if str( $DIAG ) == "true":
BARCODE_DIAG_FILE=$BARCODE_DIAG_FILE
#end if
</token>
<xml
name=
"demultiplexer_common_output_options"
>
<
param
name=
"KEEP_UNASSIGNED_READ"
type=
"boolean"
label=
"Keep unassigned reads (KEEP_UNASSIGNED_READ)"
truevalue=
"true
"
falsevalue=
"false"
checked=
"true"
/>
<section
name=
"adv_options"
title=
"Advanced Options"
expanded=
"Fals
e"
>
<
!--<section name="output_options" title="Output Options" expanded="True">-->
<param
name=
"COLLECT_OUTPUTS"
type=
"boolean
"
truevalue=
"true"
falsevalue=
"false"
checked=
"false"
label=
"Output forward and reverse reads in dataset collections"
/>
<param
name=
"KEEP_UNASSIGNED_READ"
type=
"boolean"
label=
"Keep unassigned reads (KEEP_UNASSIGNED_READ)"
truevalue=
"true"
falsevalue=
"false"
checked=
"tru
e"
/
>
<param
name=
"DIAG"
type=
"boolean"
label=
"Output barcode match reporting file (DIAG)"
truevalue=
"true"
falsevalue=
"false"
checked=
"false"
help=
"This file will
...
...
@@ -300,7 +300,7 @@ ${from_text_area}</configfile>
<param
name=
"STATS_ONLY"
type=
"boolean"
label=
"Only produce metric and diagnostic reports (STATS_ONLY)"
truevalue=
"true"
falsevalue=
"false"
checked=
"false"
help=
"do not demultiplex."
/>
</section>
<!--
</section>
-->
</xml>
<token
name=
"@common_options_cmd@"
>
...
...
@@ -333,14 +333,24 @@ ${from_text_area}</configfile>
<token
name=
"@demultiplexer_common_outputs_cmd@"
>
METRICS_FILE_NAME=$METRICS_FILE_NAME
</token>
<xml
name=
"demultiplexer_common_outputs"
>
<data
name=
"
METRICS_FILE_NAME
"
format=
"tabular"
label=
"Je-Demultiplex result"
>
<
!--<discover_datasets pattern="(?P<name>.*)\.txt" ext="fastqsanger"--
>
<data
name=
"
DEMULTIPLEX_RESULTS
"
format=
"tabular"
label=
"Je-Demultiplex result
placeholder"
hidden=
"true
"
>
<
filter>
COLLECT_OUTPUTS == False and STATS_ONLY == False
</filter
>
<discover_datasets
pattern=
"(?P<name>.*)\.txt"
directory=
"results"
visible=
"true"
ext=
"fastqsanger"
/>
</data>
<data
name=
"METRICS_FILE_NAME"
format=
"tabular"
label=
"Je-Demultiplex Metrics"
/>
<data
name=
"BARCODE_DIAG_FILE"
format=
"tabular"
label=
"Barcode statistics"
>
<filter>
(adv_options['DIAG'] == 'true')
</filter>
<filter>
DIAG
</filter>
</data>
<collection
name=
"COLLECTION_1"
type=
"list"
label=
"${tool.name} on ${on_string} : Reads_1"
>
<filter>
COLLECT_OUTPUTS and STATS_ONLY == False
</filter>
<discover_datasets
pattern=
"(?P<designation>.+_1\..+)"
ext=
"fastqsangar"
directory=
"results"
visible=
"false"
/>
</collection>
<collection
name=
"COLLECTION_2"
type=
"list"
label=
"${tool.name} on ${on_string} : Reads_2"
>
<filter>
COLLECT_OUTPUTS and STATS_ONLY == False
</filter>
<discover_datasets
pattern=
"(?P<designation>.+_2\..+)"
ext=
"fastqsangar"
directory=
"results"
visible=
"false"
/>
</collection>
</xml>
<xml
name=
"citations"
>
<citations>
...
...
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