diff mash_screen.xml @ 0:bac720dc1948 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 500478e8adcabf5249941012f78fe2140ecc7264

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mash_screen.xml	Mon Jan 07 15:09:58 2019 -0500
@@ -0,0 +1,74 @@
+<tool id="mash_screen" name="mash screen" version="@TOOL_VERSION@+galaxy0" profile="19.01">
+    <description>determines how well query sequences are contained within a pool of sequences.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">mash</requirement>
+    </requirements>
+    <version_command>mash --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$queries' queries.msh &&
+        mash screen
+             $winner_takes_all
+             -i $minimum_identity_to_report
+             -v $maximum_p_value_to_report
+             queries.msh
+             '${ str($pool).replace(',', '\' \'') }'
+             > '$output'
+    ]]></command>
+    <inputs>
+        <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."/>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="queries" value="NZ_MYON01000010.1.msh"/>
+            <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" 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"/>
+            <output name="output" file="mash_screen_NZ_MYON01000010.1_ERR024951_seqtk_sample_1000_1and2.tsv"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Description:
+
+  Determine how well query sequences are contained within a pool of sequences.
+  The queries must be formatted as a single Mash sketch file (.msh), created
+  with the `mash sketch` command. The <pool> files can be contigs or reads, in
+  fasta or fastq, gzipped or not, and "-" can be given for <pool> to read from
+  standard input. The <pool> sequences are assumed to be nucleotides, and will
+  be 6-frame translated if the <queries> are amino acids. The output fields are
+  [identity, shared-hashes, median-multiplicity, p-value, query-ID,
+  query-comment], where median-multiplicity is computed for shared hashes, based
+  on the number of observations of those hashes within the pool.
+  ]]></help>
+    <citations>
+        <citation type="bibtex">
+@article{ondov2016mash,
+  title={Mash: fast genome and metagenome distance estimation using MinHash},
+  author={Ondov, Brian D and Treangen, Todd J and Melsted, P{\'a}ll and Mallonee, Adam B and Bergman, Nicholas H and Koren, Sergey and Phillippy, Adam M},
+  journal={Genome biology},
+  volume={17},
+  number={1},
+  pages={132},
+  year={2016},
+  publisher={BioMed Central}
+  }
+	</citation>
+    </citations>
+</tool>