| Previous changeset 15:d5fe9aead222 (2017-09-26) Next changeset 17:40e1083a4430 (2017-11-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 128187381a04bed621baaee05d1b0dd55d8bd632 |
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modified:
hisat2.xml |
| b |
| diff -r d5fe9aead222 -r 21e8ea8e1adb hisat2.xml --- a/hisat2.xml Tue Sep 26 17:01:28 2017 -0400 +++ b/hisat2.xml Sat Sep 30 04:43:26 2017 -0400 |
| [ |
| @@ -290,12 +290,10 @@ --summary-file summary.txt #end if - ## Convert SAM output to sorted BAM | samtools sort - -@ \${GALAXY_SLOTS:-1} -l 6 -o '${output_alignments}' - ## Rename any output fastq files #if $output_unaligned_reads_l and $output_unaligned_reads_r: @@ -540,12 +538,12 @@ <!-- Unaligned fastq (L) --> <data name="output_unaligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: unaligned reads (L)"> - <filter>adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['unaligned_file'] is True)</filter> + <filter>adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['unaligned_file'] is True</filter> </data> <!-- Aligned fastq (L) --> <data name="output_aligned_reads_l" format="fastqsanger" label="${tool.name} on ${on_string}: aligned reads (L)"> - <filter>adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['aligned_file'] is True)</filter> + <filter>adv['output_options']['output_options_selector'] == "advanced" and adv['output_options']['aligned_file'] is True</filter> </data> <!-- Unaligned fastq (R) --> @@ -568,7 +566,8 @@ <!-- Define tests --> <tests> - <test><!-- Ensure bam output works --> + <!-- Ensure bam output works --> + <test expect_num_outputs="1" > <param name="type" value="paired" /> <param name="source" value="history" /> <param name="history_item" ftype="fasta" value="phiX.fa" /> @@ -576,14 +575,16 @@ <param name="input_2" ftype="fastqsanger" value="hisat_input_1_reverse.fastq" /> <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" /> </test> - <test><!-- Ensure built-in reference works --> + <!-- Ensure built-in reference works --> + <test expect_num_outputs="1"> <param name="type" value="paired" /> <param name="source" value="indexed" /> <param name="input_1" ftype="fastqsanger" dbkey="phiX" value="hisat_input_1_forward.fastq" /> <param name="input_2" ftype="fastqsanger" dbkey="phiX" value="hisat_input_1_reverse.fastq" /> <output name="output_alignments" file="hisat_output_1.bam" ftype="bam" lines_diff="2" /> </test> - <test><!-- Ensure trimming works --> + <!-- Ensure trimming works --> + <test expect_num_outputs="1"> <param name="type" value="paired" /> <param name="source" value="history" /> <param name="history_item" ftype="fasta" value="phiX.fa" /> @@ -594,7 +595,8 @@ <param name="input_2" ftype="fastqsanger" value="hisat_input_2_reverse.fastq" /> <output name="output_alignments" file="hisat_output_2.bam" ftype="bam" lines_diff="2" /> </test> - <test><!-- Ensure paired options works --> + <!-- Ensure paired options works --> + <test expect_num_outputs="1"> <param name="type" value="paired" /> <param name="source" value="history" /> <param name="history_item" ftype="fasta" value="phiX.fa" /> @@ -608,18 +610,19 @@ <param name="no_discordant" value="True" /> <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" /> </test> - <test><!-- Ensure unaligned output works --> + <!-- Ensure single unaligned output works --> + <test expect_num_outputs="2"> <param name="type" value="single" /> <param name="source" value="history" /> <param name="history_item" ftype="fasta" value="phiX.fa" /> <param name="output_options_selector" value="advanced" /> <param name="unaligned_file" value="true" /> - <param name="aligned_file" value="true" /> <param name="history_item" ftype="fasta" value="phiX.fa" /> <param name="input_1" ftype="fasta" value="test_unaligned_reads.fasta" /> <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" /> </test> - <test><!-- Ensure paired unaligned output works --> + <!-- Ensure paired unaligned/aligned output works --> + <test expect_num_outputs="5"> <param name="type" value="paired" /> <param name="source" value="history" /> <param name="output_options_selector" value="advanced" /> @@ -631,7 +634,8 @@ <output name="output_unaligned_reads_l" file="test_unaligned_reads.fasta" /> <output name="output_unaligned_reads_r" file="test_unaligned_reads.fasta" /> </test> - <test><!-- Ensure fastqsanger.gz works --> + <!-- Ensure fastqsanger.gz works --> + <test expect_num_outputs="1"> <param name="type" value="paired" /> <param name="source" value="history" /> <param name="history_item" ftype="fasta" value="phiX.fa" /> @@ -645,7 +649,8 @@ <param name="no_discordant" value="True" /> <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" /> </test> - <test><!-- Ensure fastqsanger.bz2 works --> + <!-- Ensure fastqsanger.bz2 works --> + <test expect_num_outputs="1"> <param name="type" value="paired" /> <param name="source" value="history" /> <param name="history_item" ftype="fasta" value="phiX.fa" /> @@ -659,7 +664,8 @@ <param name="no_discordant" value="True" /> <output name="output_alignments" file="hisat_output_3.bam" ftype="bam" lines_diff="2" /> </test> - <test><!-- Ensure paired strandness works --> + <!-- Ensure paired strandness works --> + <test expect_num_outputs="1"> <param name="type" value="paired" /> <param name="source" value="history" /> <param name="history_item" ftype="fasta" value="phiX.fa" /> @@ -668,7 +674,8 @@ <param name="rna_strandness" value="FR" /> <output name="output_alignments" file="hisat_output_4.bam" ftype="bam" lines_diff="2" /> </test> - <test><!-- Ensure summary file output works --> + <!-- Ensure summary file output works --> + <test expect_num_outputs="2"> <param name="type" value="single" /> <param name="source" value="history" /> <param name="history_item" ftype="fasta" value="phiX.fa" /> |