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Commit message:
planemo upload for repository https://github.com/katholt/srst2 commit 13ef9da7b3f4b7a06deb5b3ce7331ae127ec7aba |
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modified:
macros.xml srst2.xml |
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| diff -r 46c5d7a0393b -r 81cea47ec685 macros.xml --- a/macros.xml Tue Sep 06 14:18:05 2022 +0000 +++ b/macros.xml Mon Mar 18 12:32:11 2024 +0000 |
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| @@ -10,10 +10,15 @@ <yield/> </requirements> </xml> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">srst2</xref> + </xrefs> + </xml> <xml name="read_type_options"> <param argument="--read_type" type="select" label="Read file type"> <option value="q" selected="true">fastq</option> <option value="f">fasta</option> </param> </xml> -</macros> \ No newline at end of file +</macros> |
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| diff -r 46c5d7a0393b -r 81cea47ec685 srst2.xml --- a/srst2.xml Tue Sep 06 14:18:05 2022 +0000 +++ b/srst2.xml Mon Mar 18 12:32:11 2024 +0000 |
| [ |
| @@ -4,6 +4,7 @@ <import>macros.xml</import> <token name="@FAST_A_Q_FORMATS@">fasta,fasta.gz,fastq,fastq.gz,fastqsanger,fastqsanger.gz</token> </macros> + <expand macro="xrefs"/> <expand macro="requirements"/> <version_command>srst2 --version</version_command> <command detect_errors="exit_code"><![CDATA[ @@ -288,7 +289,7 @@ <has_n_lines n="2"/> </assert_contents> </output> - <output_collection name="new_consensus" type="list"> + <output_collection name="new_consensus" type="list" count="1"> <element name="49__AmpC1_Ecoli_Bla__AmpC1__1670.output__input.0-gene_db.pileup"> <assert_contents> <has_text text="49__AmpC1_Ecoli_Bla__AmpC1__1670"/> @@ -296,7 +297,7 @@ </assert_contents> </element> </output_collection> - <output_collection name="samtools_pileup_alignment" type="list"> + <output_collection name="samtools_pileup_alignment" type="list" count="1"> <element name="output__input.0-gene_db.pileup"> <assert_contents> <has_text text="49__AmpC1_Ecoli_Bla__AmpC1__1670"/> @@ -304,7 +305,7 @@ </assert_contents> </element> </output_collection> - <output_collection name="bowtie2_alignment_output" type="list"> + <output_collection name="bowtie2_alignment_output" type="list" count="1"> <element name="output__input.0-gene_db.sorted.bam"> <assert_contents> <has_size value="18500" delta="1000"/> @@ -347,14 +348,10 @@ <has_size value="0" delta="0"/> </assert_contents> </output> - <output_collection name="new_consensus" type="list"> - </output_collection> - <output_collection name="samtools_pileup_alignment" type="list"> - </output_collection> - <output_collection name="bowtie2_alignment_output" type="list"> - </output_collection> - <output_collection name="scores_ofEachAllele" type="list"> - </output_collection> + <output_collection name="new_consensus" type="list" count="0"/> + <output_collection name="samtools_pileup_alignment" type="list" count="0"/> + <output_collection name="bowtie2_alignment_output" type="list" count="0"/> + <output_collection name="scores_ofEachAllele" type="list" count="0"/> <output name="log_output"> <assert_contents> <has_text text="Total paired readsets found:1"/> @@ -383,4 +380,4 @@ <citations> <citation type="doi">10.1186/s13073-014-0090-6</citation> </citations> - </tool> \ No newline at end of file + </tool> |