Mercurial > repos > greg > pyfaidx
changeset 0:fb6a4e2d6234 draft default tip
Uploaded
| author | greg |
|---|---|
| date | Tue, 10 Oct 2023 13:23:15 +0000 |
| parents | |
| children | |
| files | .shed.yml macros.xml pyfaidx.xml test-data/input.fasta.gz |
| diffstat | 4 files changed, 65 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Tue Oct 10 13:23:15 2023 +0000 @@ -0,0 +1,9 @@ +name: pyfaidx +owner: greg +description: Runs faidx to index the input FASTA file. +long_description: Runs faidx to index the input FASTA file. +categories: +- Next Gen Mappers +remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/mapping/pyfaidx +homepage_url: https://github.com/gregvonkuster/galaxy_tools +type: unrestricted
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Oct 10 13:23:15 2023 +0000 @@ -0,0 +1,16 @@ +<macros> + <token name="@TOOL_VERSION@">0.7.2.2</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">21.01</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">pyfaidx</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.7287/peerj.preprints.970v1</citation> + </citations> + </xml> +</macros> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pyfaidx.xml Tue Oct 10 13:23:15 2023 +0000 @@ -0,0 +1,40 @@ +<tool id="pyfaidx" name="pyfaidx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>efficient FASTA indexing</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +#if $input.is_of_type('fasta.gz'): + gunzip -c '$input' > 'input.fasta' && +#else: + ln -s '$input' 'input.fasta' && +#end if +faidx -i chromsizes 'input.fasta' > '$output' + ]]></command> + <inputs> + <param name="input" type="data" format="fasta,fasta.gz" label="Assembled FASTA file"/> + </inputs> + <outputs> + <data name="output" format="fasta"/> + </outputs> + <tests> + <test> + <param name="input" value="input.fasta.gz" ftype="fasta.gz"/> + <output name="output" ftype="fasta"> + <assert_contents> + <has_size value="51690"/> + <has_text text=">contig_10"/> + <has_text text=">contig_7"/> + </assert_contents> + </output> + </test> + </tests> + <help> +**What it does** + +Runs faidx to index the input FASTA file. + </help> + <expand macro="citations"/> +</tool> +