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view lastz_macros.xml @ 11:37b497aa133f draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c
author | iuc |
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date | Sun, 02 Jul 2023 12:10:46 +0000 |
parents | 3e1ea2facca6 |
children |
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<macros> <token name="@TOOL_VERSION@">1.04.22</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@TARGET_INPUT_COMMAND_LINE@"><![CDATA[ #if $source.ref_source=="history": #if $source.target.is_of_type('fasta.gz'): <(gunzip -c '${source.target}') #else: '${source.target}' #end if #else: '${source.target_2bit.fields.path}' #end if ]]> </token> <token name="@query_input@"><![CDATA[ #if $query.is_of_type('fasta.gz','fastq.gz'): <(gunzip -c '${query}') #elif $query.is_of_type('fastq.bz2'): <(bunzip2 -c '${query}') #else: '${query}' #end if ]]> </token> <xml name="bio_tools"> <xrefs> <xref type="bio.tools">lastz</xref> </xrefs> </xml> <xml name="target_input"> <conditional name="source"> <param name="ref_source" type="select" label="Select TARGET sequence(s) to align against" help="If your TARGET is in history, choose 'from your history' option"> <option value="cached">locally cached</option> <option value="history">from your history</option> </param> <when value="cached"> <param name="target_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> <options from_data_table="lastz_seqs" /> </param> </when> <when value="history"> <param name="target" type="data" format="fasta,fasta.gz" label="Select a reference dataset" /> </when> </conditional> </xml> <xml name="citations"> <citations> <citation type="bibtex"> @misc{ githublastz, author = {Harris, Robert}, year = {2007}, title = {Improved pairwise alignment of genomic DNA}, publisher = {The Pennsylvania State University}, journal = {Ph. D. Thesis}, url = {http://www.bx.psu.edu/~rsharris/rsharris_phd_thesis_2007.pdf}, } </citation> </citations> </xml> </macros>