Mercurial > repos > devteam > lastz
diff lastz.xml @ 3:c3767eaae954 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413
| author | iuc |
|---|---|
| date | Thu, 17 May 2018 04:28:59 -0400 |
| parents | 8e9252994649 |
| children | 0acd9701676b |
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--- a/lastz.xml Fri Mar 02 12:06:35 2018 -0500 +++ b/lastz.xml Thu May 17 04:28:59 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="lastz_wrapper_2" name="LASTZ" version="1.3"> +<tool id="lastz_wrapper_2" name="LASTZ" version="1.3.1"> <description>: align long sequences</description> <macros> <import>lastz_macros.xml</import> @@ -7,6 +7,7 @@ <requirement type="package" version="@LASTZ_CONDA_VERSION@">lastz</requirement> <requirement type="package" version="1.7">samtools</requirement> <requirement type="package" version="3.4.2">r-base</requirement> + <requirement type="package" version="1.0.6">bzip2</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ lastz @@ -18,7 +19,7 @@ '${where_to_look.nomirror}' #end if #else: - '${query}' + @query_input@ #end if ## WHERE TO LOOK -------------------------------- @@ -279,7 +280,7 @@ </configfiles> <inputs> <expand macro="target_input"/> - <param name="query" format="fasta,fastq" type="data" label="Select QUERY sequence(s)" help="These are the sequences that you are aligning against TARGET"/> + <param name="query" format="fasta,fastq,fasta.gz,fastq.gz,fastq.bz2" type="data" label="Select QUERY sequence(s)" help="These are the sequences that you are aligning against TARGET"/> <section name="where_to_look" expanded="False" title="Where to look"> <param name="strand" type="select" display="radio" label="which strand to search" argument="--strand" help="Search both strands or choose plus or minus"> @@ -596,6 +597,38 @@ <param name="format" value="general_def" /> <output name="output" value="test3.out" /> </test> + <test> + <param name="ref_source" value="history" /> + <param name="target" value="chrM_mouse.fa.gz" /> + <param name="query" value="chrM_human.fa.gz" /> + <param name="strand" value="--strand=both" /> + <param name="format" value="blastn" /> + <output name="output" value="test4.out" /> + </test> + <test> + <param name="ref_source" value="history" /> + <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" /> + <param name="query" ftype="fastq.bz2" value="chrM_mouse.fq.bz2" /> + <param name="strand" value="--strand=both" /> + <param name="format" value="blastn" /> + <output name="output" value="test5.out" /> + </test> + <test> + <param name="ref_source" value="history" /> + <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" /> + <param name="query" ftype="fastq.gz" value="chrM_mouse.fq.gz" /> + <param name="strand" value="--strand=both" /> + <param name="format" value="blastn" /> + <output name="output" value="test5.out" /> + </test> + <test> + <param name="ref_source" value="history" /> + <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" /> + <param name="query" ftype="fastq" value="chrM_mouse.fq" /> + <param name="strand" value="--strand=both" /> + <param name="format" value="blastn" /> + <output name="output" value="test5.out" /> + </test> </tests> <help><![CDATA[