| Previous changeset 2:7f7d8b0c8517 (2020-02-16) Next changeset 4:86dec4abcea8 (2021-04-24) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit c6efcbece52dec310253537b35419839746fff7f" |
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modified:
mash_screen.xml |
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added:
test-data/test_sketches.loc tool-data/mash_sketches.loc.sample tool_data_table_conf.xml.sample |
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| diff -r 7f7d8b0c8517 -r f8e51626fc56 mash_screen.xml --- a/mash_screen.xml Sun Feb 16 17:03:45 2020 -0500 +++ b/mash_screen.xml Wed Feb 26 15:49:03 2020 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy2" profile="19.01"> +<tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy3" profile="19.01"> <description>determines how well query sequences are contained within a pool of sequences</description> <macros> <import>macros.xml</import> @@ -6,7 +6,11 @@ <expand macro="requirements" /> <expand macro="version_command" /> <command detect_errors="exit_code"><![CDATA[ - ln -s '$queries' queries.msh && + #if str( $queries_input_source.queries_input_source_selector ) == "tool_data_table": + ln -s '$queries_input_source.queries.fields.path' queries.msh && + #elif str( $queries_input_source.queries_input_source_selector ) == 'history': + ln -s '$queries_input_source.queries' queries.msh && + #end if mash screen $winner_takes_all -i $minimum_identity_to_report @@ -41,7 +45,20 @@ <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" /> + <conditional name="queries_input_source"> + <param name="queries_input_source_selector" type="select" label="Select queries from your history or use one from a tool data table?" help=""> + <option value="tool_data_table">Queries from tool data table</option> + <option selected="True" value="history">Queries from history</option> + </param> + <when value="tool_data_table"> + <param name="queries" type="select" label="Queries (Mash Sketch)"> + <options from_data_table="mash_sketches"/> + </param> + </when> + <when value="history"> + <param name="queries" type="data" format="msh" /> + </when> + </conditional> <param name="winner_takes_all" argument="-w" type="boolean" checked="true" truevalue="-w" falsevalue="" label="'Winner takes all' to remove redundancy in the result" help="If this option is not enabled, every matching strain from the same species of the reference database is reported in the result."/> <param type="float" name="minimum_identity_to_report" argument="-i" value="0." min="-1." max="1." label="Minimum identity to report" /> @@ -52,18 +69,21 @@ </outputs> <tests> <test> + <param name="queries_input_source_selector" value="history"/> <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="queries_input_source_selector" value="tool_data_table"/> + <param name="queries" value="test_sketch"/> <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_input_source_selector" value="history"/> <param name="queries" value="NZ_MYON01000010.1.msh"/> <param name="pool_input_selector" value="paired"/> <param name="pool_1" value="ERR024951_seqtk_sample_1000_1.fastq"/> |
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| diff -r 7f7d8b0c8517 -r f8e51626fc56 test-data/test_sketches.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_sketches.loc Wed Feb 26 15:49:03 2020 -0500 |
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| @@ -0,0 +1,7 @@ +# Tab separated with three columns: +# - value (Galaxy records this in the Galaxy DB) +# - name (Galaxy shows this in the UI) +# - path (path to the Mash sketch) +# +# +test_sketch "Test Sketch" ${__HERE__}/NZ_MYON01000010.1.msh |
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| diff -r 7f7d8b0c8517 -r f8e51626fc56 tool-data/mash_sketches.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/mash_sketches.loc.sample Wed Feb 26 15:49:03 2020 -0500 |
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| @@ -0,0 +1,7 @@ +# Expect three columns, tab separated, as follows: +# - value (Galaxy records this in the Galaxy DB, must be unique, suggest using a UUID) +# - name (Galaxy shows this in the UI) +# - path to sketch.msh file +# +# e.g. +# 75913ffd-ed54-4691-ba75-159ab901835e<tab>Example sketch<tab>/path/to/mash_sketches/75913ffd-ed54-4691-ba75-159ab901835e/sketch.msh |
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| diff -r 7f7d8b0c8517 -r f8e51626fc56 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Feb 26 15:49:03 2020 -0500 |
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| @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of Mash sketches in the required format --> + <table name="mash_sketches" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/mash_sketches.loc" /> + </table> +</tables> |