| Previous changeset 0:f9a0855c792d (2022-08-22) Next changeset 2:81cea47ec685 (2024-03-18) |
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Commit message:
planemo upload for repository https://github.com/katholt/srst2 commit 2e3867763a28e217bf5f44558a3f56e7efe041c5 |
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modified:
macros.xml srst2.xml |
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| diff -r f9a0855c792d -r 46c5d7a0393b macros.xml --- a/macros.xml Mon Aug 22 19:13:16 2022 +0000 +++ b/macros.xml Tue Sep 06 14:18:05 2022 +0000 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">0.2.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">20.01</token> <xml name="requirements"> <requirements> |
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| diff -r f9a0855c792d -r 46c5d7a0393b srst2.xml --- a/srst2.xml Mon Aug 22 19:13:16 2022 +0000 +++ b/srst2.xml Tue Sep 06 14:18:05 2022 +0000 |
| [ |
| @@ -21,11 +21,13 @@ ln -s $s './$i-prev_output.txt' && #end if #end for -#for $i, $s in enumerate($use_gene_db.gene_db) - #if $s - ln -s $s './$i-gene_db.fasta' && - #end if -#end for +#if $use_gene_db.selector == "yes" + #for $i, $s in enumerate($use_gene_db.gene_db) + #if $s + ln -s $s './$i-gene_db.fasta' && + #end if + #end for +#end if #if $use_mlst_db.selector == "yes" #set ext_3=$use_mlst_db.mlst_definitions.datatype.file_ext ln -s $use_mlst_db.mlst_db './mlst_db.fasta' && @@ -96,18 +98,19 @@ #if 'keep_interim_alignment' in str($output_files_selector) --keep_interim_alignment #end if +## |true here is added in order not to search for a file that is not produced at all, such that if the user provided no gene/MLST databases or there are no outputs found, the tool will run successfully and only notify the user that no outputs are found #if 'report_new_consensus' in str($output_files_selector) and $use_gene_db.selector == "yes" and $use_mlst_db.selector == "yes" -&& mkdir -p allelesOutput/ && cp *.output__input.*.pileup allelesOutput +&& mkdir -p allelesOutput/ && cp *.output__input.*.pileup allelesOutput | true #end if #if $use_gene_db.selector == "yes" and $use_gene_db.no_gene_details -&& mkdir -p geneTypingOutput/ && cp output__genes__*__results.txt geneTypingOutput && cp output__fullgenes__*__results.txt geneTypingOutput +&& mkdir -p geneTypingOutput/ && cp output__genes__*__results.txt geneTypingOutput | true && cp output__fullgenes__*__results.txt geneTypingOutput | true #end if #if 'save_scores' in str($output_files_selector) - && mkdir -p scoresOutput/ && cp *.scores scoresOutput + && mkdir -p scoresOutput/ && cp *.scores scoresOutput | true #end if #if $input.selector == "single" or $input.selector == "paired" -&& mkdir -p bowtie2Alignments/ && cp *.sorted.bam bowtie2Alignments -&& mkdir -p samtoolsPileup/ && cp output__input.*.pileup samtoolsPileup +&& mkdir -p bowtie2Alignments/ && cp *.sorted.bam bowtie2Alignments | true +&& mkdir -p samtoolsPileup/ && cp output__input.*.pileup samtoolsPileup | true #end if ]]></command> <inputs> @@ -315,6 +318,50 @@ </assert_contents> </output> </test> + <test expect_num_outputs="7"> + <param name="prob_err" value="0.01"/> + <param name="max_unaligned_overlap" value="10"/> + <param name="mapq" value="1"/> + <param name="baseq" value="20"/> + <param name="output_files_selector" value="log,save_scores,report_new_consensus,report_all_consensus"/> + <conditional name="input"> + <param name="selector" value="paired"/> + <param name="paired_input1" value="ERR024070_1_reduced_forward_reads.fastqsanger.gz"/> + <param name="paired_input2" value="ERR024070_2_reduced_reverse_reads.fastqsanger.gz"/> + <param name="merge_paired" value="false"/> + <param name="read_type" value="q"/> + </conditional> + <conditional name="use_mlst_db"> + <param name="selector" value="no"/> + </conditional> + <conditional name="use_gene_db"> + <param name="selector" value="no"/> + </conditional> + <output name="Compiled_gene_and_mlst_output"> + <assert_contents> + <has_n_lines n="0"/> + </assert_contents> + </output> + <output name="all_consensus"> + <assert_contents> + <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 name="log_output"> + <assert_contents> + <has_text text="Total paired readsets found:1"/> + <has_n_lines n="4"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ SRST2 |