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Commit message:
"planemo upload for repository https://github.com/usegalaxy-au/tools-au commit a2c67f11b7e96be2babfdf8a60cb2e2eb181ffe9" |
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modified:
cactus_cactus.xml macros.xml |
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| diff -r 8b67dd48fec1 -r 9422c5a87ee2 cactus_cactus.xml --- a/cactus_cactus.xml Tue Sep 13 00:17:17 2022 +0000 +++ b/cactus_cactus.xml Tue Sep 20 05:38:05 2022 +0000 |
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| @@ -6,25 +6,6 @@ <expand macro="xrefs"/> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ - ## Check the FASTA headers - ## This is only necessary in pangenome mode - #if $aln_mode.aln_mode_select == 'intraspecies': - #for $seq in $in_seqs: - if - #if $seq.fasta.is_of_type('fasta.gz'): - zgrep - #else - grep - #end if - "^>" $seq.fasta | grep -q "[[:space:]]" ; then - echo "Error parsing input FASTA." ; - echo "Pangenome mode fails if there are spaces in the header." ; - echo "Please remove them with the NormalizeFasta tool." ; - exit 1 - ; fi && - #end for - #end if - ## Set up seqfile #if $aln_mode.aln_mode_select == 'interspecies': @@ -190,8 +171,8 @@ </assert_contents> </output> </test> - <!-- FASTA header --> - <test expect_exit_code="1" expect_failure="true"> + <!-- FASTA header with spaces (used to fail) --> + <test expect_num_outputs="1"> <conditional name="aln_mode"> <param name="aln_mode_select" value="intraspecies"/> </conditional> @@ -203,6 +184,11 @@ <param name="label" value="badheader2"/> <param name="fasta" value="bh2.fasta.gz"/> </repeat> + <output name="out_hal"> + <assert_contents> + <has_size value="3382274" delta="200000" /> + </assert_contents> + </output> </test> </tests> <help><![CDATA[ @@ -241,9 +227,6 @@ pangenome mode, select ‘Within-species’ in the ‘Alignment mode’ dropdown. -⚠️ To use pangenome mode, you will have to remove spaces from the headers in your FASTA file. -You can do this with the NormalizeFasta tool. - **Input** The developers recommend soft-masking your genomes with RepeatMasker |
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| diff -r 8b67dd48fec1 -r 9422c5a87ee2 macros.xml --- a/macros.xml Tue Sep 13 00:17:17 2022 +0000 +++ b/macros.xml Tue Sep 20 05:38:05 2022 +0000 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.2.1</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">20.09</token> <token name="@DIGEST@">e871d782967a66d29488e4f6971aafb4568407f6d6833010bb521cba79e61500</token> <xml name="requirements"> |