| Previous changeset 22:c3dd1aeb7d07 (2018-04-12) Next changeset 24:017aba02828d (2019-04-04) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit d611e968158b012c10d3f8b661af1f07313f06d7 |
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modified:
bowtie2_macros.xml bowtie2_wrapper.xml |
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| diff -r c3dd1aeb7d07 -r 17062a0decb7 bowtie2_macros.xml --- a/bowtie2_macros.xml Thu Apr 12 17:42:40 2018 -0400 +++ b/bowtie2_macros.xml Wed Jun 06 17:23:32 2018 -0400 |
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| @@ -323,4 +323,20 @@ <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc (possibly with -gz or -bz2); This triggers --un parameter for single reads and --un-conc for paired reads" /> <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" help="--al/--al-conc (possibly with -gz or -bz2); This triggers --al parameter for single reads and --al-conc for paired reads" /> </xml> + <xml name="dbKeyActions"> + <conditional name="reference_genome.source"> + <when value="indexed"> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="bowtie2_indexes" column="1"> + <filter type="param_value" ref="reference_genome.index" column="0"/> + </option> + </action> + </when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" /> + </action> + </when> + </conditional> + </xml> </macros> |
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| diff -r c3dd1aeb7d07 -r 17062a0decb7 bowtie2_wrapper.xml --- a/bowtie2_wrapper.xml Thu Apr 12 17:42:40 2018 -0400 +++ b/bowtie2_wrapper.xml Wed Jun 06 17:23:32 2018 -0400 |
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| @@ -557,6 +557,7 @@ </action> </when> </conditional> + <expand macro="dbKeyActions" /> </actions> </data> <data format="fastqsanger" name="output_aligned_reads_l" label="${tool.name} on ${on_string}: aligned reads (L)" > @@ -579,6 +580,7 @@ </action> </when> </conditional> + <expand macro="dbKeyActions" /> </actions> </data> <data format="fastqsanger" name="output_aligned_reads_r" label="${tool.name} on ${on_string}: aligned reads (R)"> @@ -596,6 +598,7 @@ </action> </when> </conditional> + <expand macro="dbKeyActions" /> </actions> </data> <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)"> @@ -613,6 +616,7 @@ </action> </when> </conditional> + <expand macro="dbKeyActions" /> </actions> </data> <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (BAM)"> @@ -636,6 +640,7 @@ </action> </when> </conditional> + <expand macro="dbKeyActions" /> </actions> </data> <data format="sam" name="output_sam" label="${tool.name} on ${on_string}: aligned reads (SAM)"> @@ -656,10 +661,14 @@ </action> </when> </conditional> + <expand macro="dbKeyActions" /> </actions> </data> <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats"> <filter>save_mapping_stats is True</filter> + <actions> + <expand macro="dbKeyActions" /> + </actions> </data> </outputs> <tests> |