Mercurial > repos > iuc > mash
changeset 1:402b67d1af7d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 91435d801528addac840722e9a0092b2d342b8bb
| author | iuc |
|---|---|
| date | Wed, 23 Jan 2019 15:59:25 -0500 |
| parents | bac720dc1948 |
| children | 7f7d8b0c8517 |
| files | mash_screen.xml |
| diffstat | 1 files changed, 33 insertions(+), 5 deletions(-) [+] |
line wrap: on
line diff
--- a/mash_screen.xml Mon Jan 07 15:09:58 2019 -0500 +++ b/mash_screen.xml Wed Jan 23 15:59:25 2019 -0500 @@ -1,4 +1,4 @@ -<tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy0" profile="19.01"> +<tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy1" profile="19.01"> <description>determines how well query sequences are contained within a pool of sequences.</description> <macros> <import>macros.xml</import> @@ -14,12 +14,36 @@ -i $minimum_identity_to_report -v $maximum_p_value_to_report queries.msh - '${ str($pool).replace(',', '\' \'') }' + #if str( $pool_input.pool_input_selector ) == "paired" + '$pool_input.pool_1' '$pool_input.pool_2' + #end if + #if str( $pool_input.pool_input_selector ) == "paired_collection" + '$pool_input.pool.forward' '$pool_input.pool.reverse' + #end if + #if str( $pool_input.pool_input_selector ) == "single" + '$pool_input.pool' + #end if > '$output' ]]></command> <inputs> + <conditional name="pool_input"> + <param name="pool_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data"> + <option value="paired">Paired</option> + <option value="single">Single</option> + <option value="paired_collection">Paired Collection</option> + </param> + <when value="paired"> + <param name="pool_1" type="data" format="@INTYPES@" label="Select first set of reads" help="Specify dataset with forward reads"/> + <param name="pool_2" type="data" format="@INTYPES@" label="Select second set of reads" help="Specify dataset with reverse reads"/> + </when> + <when value="single"> + <param name="pool" type="data" format="@INTYPES@" label="Select fastq dataset" help="Specify dataset with single reads"/> + </when> + <when value="paired_collection"> + <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="msh" /> - <param type="data" multiple="true" name="pool" format="@INTYPES@" /> <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."/> @@ -30,17 +54,21 @@ <tests> <test> <param name="queries" value="NZ_MYON01000010.1.msh"/> + <param name="pool_input_selector" value="single"/> <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq"/> <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1.tsv"/> </test> <test> <param name="queries" value="NZ_MYON01000010.1.msh"/> + <param name="pool_input_selector" value="single"/> <param name="pool" value="ERR024951_seqtk_sample_1000_2.fastq"/> <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_2.tsv"/> </test> <test> <param name="queries" value="NZ_MYON01000010.1.msh"/> - <param name="pool" value="ERR024951_seqtk_sample_1000_1.fastq,ERR024951_seqtk_sample_1000_2.fastq"/> + <param name="pool_input_selector" value="paired"/> + <param name="pool_1" value="ERR024951_seqtk_sample_1000_1.fastq"/> + <param name="pool_2" value="ERR024951_seqtk_sample_1000_2.fastq"/> <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/> </test> </tests> @@ -69,6 +97,6 @@ year={2016}, publisher={BioMed Central} } - </citation> + </citation> </citations> </tool>