Mercurial > repos > devteam > sam_to_bam
changeset 9:d83ad701f011 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
| author | iuc |
|---|---|
| date | Sat, 27 Nov 2021 12:27:56 +0000 |
| parents | c701f5f96f32 |
| children | 157bab484e81 |
| files | macros.xml sam_to_bam.xml test-data/chr_m.bgzipped_fasta.gz test-data/chr_m.fasta.gz |
| diffstat | 4 files changed, 62 insertions(+), 15 deletions(-) [+] |
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--- a/macros.xml Tue Sep 28 15:58:15 2021 +0000 +++ b/macros.xml Sat Nov 27 12:27:56 2021 +0000 @@ -50,23 +50,56 @@ #end for ]]></token> <token name="@PREPARE_FASTA_IDX@"><![CDATA[ - ##checks for reference data ($addref_cond.addref_select=="history" or =="cached") - ##and sets the -t/-T parameters accordingly: - ##- in case of history a symbolic link is used because samtools (view) will generate - ## the index which might not be possible in the directory containing the fasta file - ##- in case of cached the absolute path is used which allows to read the cram file - ## without specifying the reference + ## Make the user-selected reference genome, if any, accessible through + ## a shell variable $reffa, index the reference if necessary, and make + ## the fai-index file available through a shell variable $reffai. + + ## For a cached genome simply sets the shell variables to point to the + ## genome file and its precalculated index. + ## For a genome from the user's history, if that genome is a plain + ## fasta file, the code creates a symlink in the pwd, creates the fai + ## index file next to it, then sets the shell variables to point to the + ## symlink and its index. + ## For a fasta.gz dataset from the user's history, it tries the same, + ## but this will only succeed if the file got compressed with bgzip. + ## For a regular gzipped file samtools faidx will fail, in which case + ## the code falls back to decompressing to plain fasta before + ## reattempting the indexing. + ## Indexing of a bgzipped file produces a regular fai index file *and* + ## a compressed gzi file. The former is identical to the fai index of + ## the uncompressed fasta. + + ## If the user has not selected a reference (it's an optional parameter + ## in some samtools wrappers), a cheetah boolean use_ref is set to + ## False to encode that fact. + + #set use_ref=True #if $addref_cond.addref_select == "history": - ln -s '${addref_cond.ref}' reference.fa && - samtools faidx reference.fa && - #set reffa="reference.fa" - #set reffai="reference.fa.fai" + #if $addref_cond.ref.is_of_type('fasta'): + reffa="reference.fa" && + ln -s '${addref_cond.ref}' \$reffa && + samtools faidx \$reffa && + #else: + reffa="reference.fa.gz" && + ln -s '${addref_cond.ref}' \$reffa && + { + samtools faidx \$reffa || + { + echo "Failed to index compressed reference. Trying decompressed ..." 1>&2 && + gzip -dc \$reffa > reference.fa && + reffa="reference.fa" && + samtools faidx \$reffa; + } + } && + #end if + reffai=\$reffa.fai && #elif $addref_cond.addref_select == "cached": - #set reffa=str($addref_cond.ref.fields.path) - #set reffai=str($addref_cond.ref.fields.path)+".fai" + ## in case of cached the absolute path is used which allows to read + ## a cram file without specifying the reference + reffa='${addref_cond.ref.fields.path}' && + reffai=\$reffa.fai && #else - #set reffa=None - #set reffai=None + #set use_ref=False #end if ]]></token>
--- a/sam_to_bam.xml Tue Sep 28 15:58:15 2021 +0000 +++ b/sam_to_bam.xml Sat Nov 27 12:27:56 2021 +0000 @@ -16,7 +16,7 @@ samtools view -b -@ \$addthreads - -t '$reffai' + -t "\$reffai" '$input' | samtools sort @@ -67,6 +67,20 @@ <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" /> <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/> </test> + <test> + <!-- Test direct use of bgzipped reference --> + <param name="addref_select" value="history" /> + <param name="ref" ftype="fasta.gz" dbkey="equCab2" value="chr_m.bgzipped_fasta.gz" /> + <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" /> + <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/> + </test> + <test> + <!-- Test with simple gzipped reference, which requires decompression --> + <param name="addref_select" value="history" /> + <param name="ref" ftype="fasta.gz" dbkey="equCab2" value="chr_m.fasta.gz" /> + <param name="input" ftype="sam" value="sam_to_bam_noheader_in2.sam" /> + <output name="output1" ftype="bam" file="sam_to_bam_out3.bam" lines_diff="4"/> + </test> </tests> <help><![CDATA[ **What it does**