| Previous changeset 2:b6abccb1f25b (2021-04-25) Next changeset 4:42126b414951 (2021-06-03) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e" |
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modified:
pangolin.xml |
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added:
test-data/multiple_alignment.fasta.gz |
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removed:
test-data/result1.tsv |
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| diff -r b6abccb1f25b -r 514a786baaa9 pangolin.xml --- a/pangolin.xml Sun Apr 25 20:46:03 2021 +0000 +++ b/pangolin.xml Wed May 19 13:32:34 2021 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@" profile="20.01"> +<tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy1" profile="20.01"> <description>Phylogenetic Assignment of Outbreak Lineages</description> <macros> <token name="@TOOL_VERSION@">2.3.8</token> @@ -23,20 +23,26 @@ --max-ambig $max_ambig --min-length $min_length '$input1' - && csvtk csv2tab report.csv | tail -n-1 >'$output1' + && csvtk csv2tab report.csv + #if not $include_header: + | tail -n+2 + #end if + > '$output1' #if $alignment && mv sequences.aln.fasta '$align1' #end if ]]></command> <inputs> - <param type="data" name="input1" format="fasta" label="Input FASTA File(s)" /> - <param name="alignment" type="boolean" label="Generate output alignment" + <param type="data" name="input1" format="fasta" label="Input FASTA File(s)" /> + <param name="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" /> - <param argument="--min-length" type="integer" label="Minimum query length allowed" - value="10000" min="0" help="Minimum query length allowed for pangolin to attempt assignment"/> - <conditional name="db"> + <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" /> + <param argument="--min-length" type="integer" label="Minimum query length allowed" + value="10000" min="0" help="Minimum query length allowed for pangolin to attempt assignment"/> + <param name="include_header" type="boolean" label="Include header line in output file" + truevalue="true" falsevalue="false" /> + <conditional name="db"> <param type="select" name="source" label="pangoLEARN source" help="Where to find the pangoLEARN database"> <option value="download">Download latest from web</option> <option value="builtin">Use database from Galaxy server</option> @@ -49,7 +55,7 @@ <options from_data_table="pangolearn"> <column name="value" index="0" /> <column name="name" index="1" /> - <column name="path" index="3" /> + <column name="path" index="3" /> <filter type="sort_by" column="0"/> </options> </param> @@ -69,43 +75,83 @@ </data> </outputs> <tests> - <test expect_num_outputs="1"> - <param name="input1" value="test1.fasta"/> - <conditional name="db"> - <param name="source" value="download" /> - </conditional> - <output name="output1"> - <assert_contents> - <has_text text="B.1.1" /> - <has_text text="passed_qc" /> - </assert_contents> - </output> - </test> - <test expect_num_outputs="2"> - <param name="alignment" value="--alignment" /> - <param name="input1" value="test1.fasta" /> - <conditional name="db"> - <param name="source" value="download" /> - </conditional> - <output name="output1"> - <assert_contents> - <has_text text="B.1.1" /> - <has_text text="passed_qc" /> - </assert_contents> - </output> - <output name="align1" file="aln1.fasta" ftype="fasta" /> - </test> - <test expect_num_outputs="1"> - <param name="input1" value="test1.fasta"/> - <conditional name="db"> - <param name="source" value="builtin" /> - </conditional> - <output name="output1"> - <assert_contents> - <has_text text="2021-04-21" /> - </assert_contents> - </output> - </test> + <test expect_num_outputs="1"> + <param name="input1" value="test1.fasta"/> + <conditional name="db"> + <param name="source" value="download" /> + </conditional> + <output name="output1" ftype="tabular"> + <assert_contents> + <has_text text="B.1.1" /> + <has_text text="passed_qc" /> + <has_n_lines n="1" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="2"> + <param name="alignment" value="--alignment" /> + <param name="input1" value="test1.fasta" /> + <conditional name="db"> + <param name="source" value="download" /> + </conditional> + <output name="output1" ftype="tabular"> + <assert_contents> + <has_text text="B.1.1" /> + <has_text text="passed_qc" /> + <has_n_lines n="1" /> + </assert_contents> + </output> + <output name="align1" file="aln1.fasta" ftype="fasta"> + <assert_contents> + <has_text text="Consensus_EB232-crude-prep_S297" /> + <has_n_lines n="2" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input1" value="test1.fasta"/> + <conditional name="db"> + <param name="source" value="builtin" /> + </conditional> + <output name="output1" ftype="tabular"> + <assert_contents> + <has_text text="Consensus_EB232-crude-prep_S297" /> + <has_n_lines n="1" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input1" value="multiple_alignment.fasta.gz"/> + <conditional name="db"> + <param name="source" value="builtin" /> + </conditional> + <output name="output1" ftype="tabular"> + <assert_contents> + <has_text text="Serbia" /> + <has_text text="Poland" /> + <has_text text="USA" /> + <has_n_lines n="34" /> + </assert_contents> + </output> + </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" /> + </conditional> + <output name="output1" ftype="tabular"> + <assert_contents> + <has_text text="pangoLEARN_version" /> + <has_text text="lineage" /> + <has_text text="Serbia" /> + <has_text text="Poland" /> + <has_text text="USA" /> + <has_n_lines n="35" /> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ |
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| diff -r b6abccb1f25b -r 514a786baaa9 test-data/multiple_alignment.fasta.gz |
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| Binary file test-data/multiple_alignment.fasta.gz has changed |
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| diff -r b6abccb1f25b -r 514a786baaa9 test-data/result1.tsv --- a/test-data/result1.tsv Sun Apr 25 20:46:03 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -Consensus_EB232-crude-prep_S297.primertrimmed.consensus_threshold_0.75_quality_20 B.1.1 1.0 2021-04-14 passed_qc |