Mercurial > repos > gbcs-embl-heidelberg > je_clip
changeset 2:b61628ae2371 draft
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 62411561ae3bc65ea8762d27ec79a7d912503e5b
| author | gbcs-embl-heidelberg |
|---|---|
| date | Wed, 07 Dec 2016 11:57:50 -0500 |
| parents | dfacabbde112 |
| children | 2cfed59e4d27 |
| files | je-clip.xml macros.xml test-data/markdupes_DNase_sorted.bam |
| diffstat | 3 files changed, 18 insertions(+), 14 deletions(-) [+] |
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--- a/je-clip.xml Thu Nov 26 08:59:38 2015 -0500 +++ b/je-clip.xml Wed Dec 07 11:57:50 2016 -0500 @@ -21,7 +21,7 @@ @barcode_len_cmd@ ADD=${ADD} #if str($ADD) == "false": - BARCODE_RESULT_FILENAME=$BARCODE_RESULT_FILENAME + BARCODE_RESULT_FILENAME=${BARCODE_RESULT_FILENAME} #end if OF1=${OF1} @@ -54,10 +54,12 @@ </inputs> <outputs> - <data name="BARCODE_RESULT_FILENAME" format="tabular" label="Je-Clipped Barcodes"/> - <data name="OF1" format_source="input_1" label="Je-Clipped {on_string}"/> - <data name="OF2" format_source="input_1" label="Je-Clipped {on_string}"> - <filter>(type != "single")</filter> + <data name="BARCODE_RESULT_FILENAME" format="tabular" label="Je-Clipped Barcodes"> + <filter>!ADD</filter> + </data> + <data name="OF1" format_source="input_1" label="Je-Clip OF1: ${on_string}"/> + <data name="OF2" format_source="input_2" label="Je-Clip OF2: ${on_string}"> + <filter>library["type"] != "single"</filter> </data> </outputs>
--- a/macros.xml Thu Nov 26 08:59:38 2015 -0500 +++ b/macros.xml Wed Dec 07 11:57:50 2016 -0500 @@ -17,8 +17,8 @@ <xml name="paired_options"> <when value="paired"> - <param name="input_1" format="fastq" type="data" label="FASTQ file #1"/> - <param name="input_2" format="fastq" type="data" label="FASTQ file #2"/> + <param name="input_1" format="fastq,gz" type="data" label="FASTQ file #1"/> + <param name="input_2" format="fastq,gz" type="data" label="FASTQ file #2"/> <yield /> <param name="SAME_HEADERS" type="boolean" label="Ensure headers of both reads of a pair are identical (SAME_HEADERS)" @@ -27,7 +27,7 @@ falsevalue="false" checked="false"/> </when> <when value="paired_collection"> - <param name="input_1" format="fastq" type="data_collection" collection_type="paired" + <param name="input_1" format="fastq,gz" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset"/> <yield /> <param name="SAME_HEADERS" type="boolean" @@ -60,18 +60,18 @@ <option value="paired_collection">Paired-end Dataset Collection</option> </param> <when value="single"> - <param name="input_1" format="fastq" type="data" label="FASTQ file"/> - <param name="I1" type="data" format="fastq" label="First Index File"/> + <param name="input_1" format="fastq,gz" type="data" label="FASTQ file"/> + <param name="I1" type="data" format="fastq,gz" label="First Index File"/> </when> <expand macro="paired_options"> - <param name="I1" type="data" format="fastq" label="First Index File"/> + <param name="I1" type="data" format="fastq,gz" label="First Index File"/> <conditional name="I2_CONDITIONAL"> <param name="I2_AVAILABLE" type="select" label="Do you have a second index file?"> <option value="true">Yes</option> <option value="false" selected="true">No</option> </param> <when value="true"> - <param name="I2" type="data" format="fastq" label="Second Index File"/> + <param name="I2" type="data" format="fastq,gz" label="Second Index File"/> <expand macro="bred_conditional"/> </when> <when value="false"/> @@ -88,7 +88,7 @@ <option value="paired_collection">Paired-end Dataset Collection</option> </param> <when value="single"> - <param name="input_1" format="fastq" type="data" label="FASTQ file"/> + <param name="input_1" format="fastq,gz" type="data" label="FASTQ file"/> </when> <expand macro="paired_options"> <yield /> @@ -298,6 +298,8 @@ ZT=${ZT} #if str( $RCHAR ) != "": RCHAR=${RCHAR} + #else: + RCHAR=null #end if GZ=${GZ} OUTPUT_DIR=results @@ -310,7 +312,7 @@ <param name="RCHAR" type="text" label="Replace white space in the read name/header with speficied symbols (RCHAR)" - help="Set to empty for no replacement" + help="Set to empty or null for no replacement." value=":"/> <param name="GZ" type="boolean" hidden="true" label="Compress output (GZ)"