| Previous changeset 9:aec58624706f (2019-12-04) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 3a94fbf6a188ea81441ef2f654ba5a74bff56f22 |
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modified:
kraken.xml macros.xml |
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| diff -r aec58624706f -r 766d5f63b0f4 kraken.xml --- a/kraken.xml Wed Dec 04 06:51:45 2019 -0500 +++ b/kraken.xml Tue Mar 12 16:10:22 2024 +0000 |
| b |
| @@ -6,6 +6,7 @@ <macros> <import>macros.xml</import> </macros> + <expand macro="xrefs"/> <expand macro="requirements" /> <expand macro="version_command" /> <command detect_errors="exit_code"> @@ -66,7 +67,7 @@ </param> <when value="collection"> <param format="fasta,fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTA or FASTQ datasets" /> - <param name="check_names" argument="--check-names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match"/> + <param argument="--check-names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match"/> </when> <when value="yes"> <param format="fasta,fastq" name="forward_input" type="data" label="Forward strand" help="FASTA or FASTQ dataset"/> @@ -87,13 +88,13 @@ <option selected="True" value="no">No</option> </param> <when value="yes"> - <param name="min_hits" argument="--min-hits" type="integer" value="1" label="Number of hits required for classification" + <param argument="--min-hits" type="integer" value="1" label="Number of hits required for classification" help="min-hits will allow you to require multiple hits before declaring a sequence classified, which can be especially useful with custom databases when testing to see if sequences either do or do not belong to a particular genome; default=1"/> </when> <when value="no"/><!-- Do absolutely nothing --> </conditional> - <param name="only_classified_output" argument="--only-classified-output" type="boolean" checked="False" truevalue="--only-classified-output" falsevalue="" + <param argument="--only-classified-output" type="boolean" checked="False" truevalue="--only-classified-output" falsevalue="" label="Print no Kraken output for unclassified sequences"/> <expand macro="input_database" /> @@ -110,7 +111,7 @@ </outputs> <tests> - <test> + <test expect_num_outputs="1"> <param name="single_paired_selector" value="no"/> <param name="input_sequences" value="kraken/kraken_test1.fa" ftype="fasta"/> <param name="split_reads" value="false"/> @@ -119,7 +120,7 @@ <param name="kraken_database" value="old_style_test_entry"/> <output name="output" file="kraken/kraken_test1_output.tab" ftype="tabular"/> </test> - <test> + <test expect_num_outputs="1"> <param name="single_paired_selector" value="no"/> <param name="input_sequences" value="kraken/kraken_test1.fa" ftype="fasta"/> <param name="split_reads" value="false"/> |
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| diff -r aec58624706f -r 766d5f63b0f4 macros.xml --- a/macros.xml Wed Dec 04 06:51:45 2019 -0500 +++ b/macros.xml Tue Mar 12 16:10:22 2024 +0000 |
| [ |
| @@ -6,6 +6,11 @@ <requirement type="package" version="1.1.1">kraken</requirement> </requirements> </xml> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">kraken</xref> + </xrefs> + </xml> <xml name="version_command"> <version_command><![CDATA[ export LC_ALL=C && kraken --version |