Mercurial > repos > dfornika > mash
changeset 7:cf0d6a872bd4 draft
planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/mash commit 423cf96266f6ac433052ff72edb1397502313010-dirty
author | dfornika |
---|---|
date | Thu, 25 Jul 2019 15:31:50 -0400 |
parents | 948dba53a391 |
children | 0586ef4759e5 |
files | mash_dist.xml mash_screen.xml |
diffstat | 2 files changed, 12 insertions(+), 4 deletions(-) [+] |
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--- a/mash_dist.xml Tue Jan 29 14:58:37 2019 -0500 +++ b/mash_dist.xml Thu Jul 25 15:31:50 2019 -0400 @@ -31,7 +31,11 @@ > '$output' ]]></command> <inputs> - <param name="reference" type="data" format="@INTYPES@,binary" /> + <param name="reference" type="select"> + <options from_data_table="mash_sketches"> + <validator type="no_options" message="No Mash sketches are available." /> + </options> + </param> <conditional name="query_input"> <param name="query_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data"> <option value="paired">Paired</option> @@ -46,7 +50,7 @@ <when value="single"> <param name="query" type="data" format="@INTYPES@" label="Select fastq dataset" help="Specify dataset with single reads"/> </when> - <when value="collection"> + <when value="collection"> <param name="query" format="@INTYPES@" type="data_collection" collection_type="list" label="Select a collection" help="See help section for an explanation of dataset collections"/> </when> <when value="paired_collection">
--- a/mash_screen.xml Tue Jan 29 14:58:37 2019 -0500 +++ b/mash_screen.xml Thu Jul 25 15:31:50 2019 -0400 @@ -8,7 +8,7 @@ </requirements> <version_command>mash --version</version_command> <command detect_errors="exit_code"><![CDATA[ - ln -s '$queries' queries.msh && + ln -s '${queries}/sketch.msh' queries.msh && mash screen $winner_takes_all -i $minimum_identity_to_report @@ -43,7 +43,11 @@ <param name="pool" format="@INTYPES@" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> </when> </conditional> - <param name="queries" type="data" format="binary" /> + <param name="queries" type="select"> + <options from_data_table="mash_sketches"> + <validator type="no_options" message="No mash sketches are available." /> + </options> + </param> <param type="boolean" name="winner_takes_all" argument="-w" truevalue="-w" falsevalue=""/> <param type="float" name="minimum_identity_to_report" argument="-i" value="0." min="-1." max="1." /> <param type="float" name="maximum_p_value_to_report" argument="-v" value="1." min="0." max="1."/>