Mercurial > repos > iuc > pangolin
diff pangolin.xml @ 4:42126b414951 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
author | iuc |
---|---|
date | Thu, 03 Jun 2021 06:38:26 +0000 |
parents | 514a786baaa9 |
children | 42a174224817 |
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--- a/pangolin.xml Wed May 19 13:32:34 2021 +0000 +++ b/pangolin.xml Thu Jun 03 06:38:26 2021 +0000 @@ -1,7 +1,7 @@ -<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy1" profile="20.01"> +<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01"> <description>Phylogenetic Assignment of Outbreak Lineages</description> <macros> - <token name="@TOOL_VERSION@">2.3.8</token> + <token name="@TOOL_VERSION@">3.0.3</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement> @@ -18,6 +18,7 @@ #if str($db.source) == "download" or str($db.source) == "builtin" --datadir 'datadir' #end if + $usher $alignment --outfile report.csv --max-ambig $max_ambig @@ -34,7 +35,8 @@ ]]></command> <inputs> <param type="data" name="input1" format="fasta" label="Input FASTA File(s)" /> - <param name="alignment" type="boolean" label="Generate output alignment" + <param argument="--usher" type="boolean" label="Use UShER model" truevalue="--usher" falsevalue="" help="Use UShER model instead of default pangoLEARN model" /> + <param argument="--alignment" type="boolean" label="Generate output alignment" truevalue="--alignment" falsevalue="" /> <param argument="--max-ambig" type="float" label="Maximum proportion of Ns allowed" value="0.5" min="0" max="1" help="Maximum proportion of Ns allowed for pangolin to attempt assignment" /> @@ -56,7 +58,8 @@ <column name="value" index="0" /> <column name="name" index="1" /> <column name="path" index="3" /> - <filter type="sort_by" column="0"/> + <filter type="sort_by" column="0" /> + <filter type="static_value" column="2" value="3.0" /> </options> </param> </when> @@ -67,7 +70,7 @@ <outputs> <data name="output1" format="tabular" label="pangolin on ${on_string}"> <actions> - <action name="column_names" type="metadata" default="taxon,lineage,probability,pangoLEARN_version,status,note" /> + <action name="column_names" type="metadata" default="taxon,lineage,conflict,ambiguity_score,scorpio_call,scorpio_support,scorpio_conflict,version,pangolin_version,pangoLEARN_version,pango_version,status,note" /> </actions> </data> <data name="align1" format="fasta" label="pangolin alignment on ${on_string}"> @@ -82,7 +85,22 @@ </conditional> <output name="output1" ftype="tabular"> <assert_contents> - <has_text text="B.1.1" /> + <has_text_matching expression="B.1.1\t0.0" /> + <has_text text="passed_qc" /> + <has_n_lines n="1" /> + </assert_contents> + </output> + </test> + <!-- test UShER mode --> + <test expect_num_outputs="1"> + <param name="input1" value="test1.fasta"/> + <param name="usher" value="true" /> + <conditional name="db"> + <param name="source" value="download" /> + </conditional> + <output name="output1" ftype="tabular"> + <assert_contents> + <has_text_matching expression="B.1.1.409\t\t*PUSHER" /> <has_text text="passed_qc" /> <has_n_lines n="1" /> </assert_contents> @@ -96,7 +114,7 @@ </conditional> <output name="output1" ftype="tabular"> <assert_contents> - <has_text text="B.1.1" /> + <has_text_matching expression="B.1.1\t0.0" /> <has_text text="passed_qc" /> <has_n_lines n="1" /> </assert_contents> @@ -108,7 +126,8 @@ </assert_contents> </output> </test> - <test expect_num_outputs="1"> + <!-- testing with builtin data is too large --> + <!-- <test expect_num_outputs="1"> <param name="input1" value="test1.fasta"/> <conditional name="db"> <param name="source" value="builtin" /> @@ -119,7 +138,7 @@ <has_n_lines n="1" /> </assert_contents> </output> - </test> + </test> <test expect_num_outputs="1"> <param name="input1" value="multiple_alignment.fasta.gz"/> <conditional name="db"> @@ -133,13 +152,13 @@ <has_n_lines n="34" /> </assert_contents> </output> - </test> + </test> --> <!-- test include-header option --> <test expect_num_outputs="1"> <param name="input1" value="multiple_alignment.fasta.gz"/> <param name="include_header" value="true" /> <conditional name="db"> - <param name="source" value="builtin" /> + <param name="source" value="download" /> </conditional> <output name="output1" ftype="tabular"> <assert_contents>