| Previous changeset 6:7e47f78590cc (2017-09-15) Next changeset 8:a79f67128fc3 (2018-04-23) |
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Commit message:
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750 |
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modified:
macros.xml |
| b |
| diff -r 7e47f78590cc -r eb38b7dc3810 macros.xml --- a/macros.xml Fri Sep 15 08:18:18 2017 -0400 +++ b/macros.xml Mon Mar 05 07:13:20 2018 -0500 |
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| @@ -1,6 +1,6 @@ <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 @@ </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="False"> + <!--<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="true"/> <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 @@ <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 @@ <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> |