Mercurial > repos > yating-l > ucsc_blat
changeset 12:e79965d0351c draft
planemo upload commit 6358ce7c332f42526423d365f06516983ca677a0
| author | iuc |
|---|---|
| date | Sat, 03 Dec 2022 10:38:40 +0000 |
| parents | 2a89f630fa85 |
| children | 820f68ad34a7 |
| files | blat.xml test-data/mini-db.fa.gz test-data/mini-query.fa.gz |
| diffstat | 3 files changed, 41 insertions(+), 6 deletions(-) [+] |
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--- a/blat.xml Fri Dec 02 09:35:54 2022 +0000 +++ b/blat.xml Sat Dec 03 10:38:40 2022 +0000 @@ -2,7 +2,7 @@ <description>BLAST-like sequence alignment tool</description> <macros> <token name="@TOOL_VERSION@">377</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="mask_cond" tokens="maskarg,label,help"> <conditional name="@MASKARG@_type"> @@ -30,7 +30,9 @@ <command detect_errors="exit_code"><![CDATA[ #if str($reference_source.reference_source_selector) == "history": ## blat depends on file extension - #if $reference_source.database.is_of_type("fasta"): + #if $reference_source.database.is_of_type("fasta.gz"): + #set $reference_fasta_filename = "localref.fa.gz" + #elif $reference_source.database.is_of_type("fasta"): #set $reference_fasta_filename = "localref.fa" #elif $reference_source.database.is_of_type("twobit"): #set $reference_fasta_filename = "localref.2bit" @@ -42,6 +44,18 @@ #set $reference_fasta_filename = str($reference_source.database.fields.path) #end if + ## blat depends on file extension + #if $query.is_of_type("fasta.gz"): + #set $query_filename = "query.fa.gz" + #elif $query.is_of_type("fasta"): + #set $query_filename = "query.fa" + #elif $query.is_of_type("twobit"): + #set $query_filename = "query.2bit" + #else + #set $query_filename = "query" + #end if + ln -s '$query' '$query_filename' && + blat -q=$query_type -t=$database_type @@ -100,7 +114,7 @@ -dots=$dots #end if '$reference_fasta_filename' - '$query' + '$query_filename' -out=$out '$output' ]]></command> @@ -121,10 +135,10 @@ </param> </when> <when value="history"> - <param name="database" type="data" format="fasta,twobit" label="Using database file, either a .fa, .nib or .2bit file" /> + <param name="database" type="data" format="fasta,fasta.gz,twobit" label="Using database file, either a fasta, fasta.gz or twobit dataset" /> </when> </conditional> - <param name="query" type="data" format="fasta, twobit" label="Query data, either a .fa, .nib or .2bit file"/> + <param name="query" type="data" format="fasta,fasta.gz,twobit" label="Query data, either a fasta, fasta.gz or twobit dataset"/> <param argument="-t" name="database_type" type="select" format="txt" multiple="false" label="database type" help="Choose your database type, the default is dnax"> <option value="dna" selected="true">dna - DNA sequence</option> <option value="prot">prot - protein sequence</option> @@ -259,7 +273,28 @@ <has_text text="-mask='/"/> </assert_command> </test> - </tests> + <!-- tiny test data from https://davetang.org/muse/2012/05/15/using-blat/ --> + <test> + <conditional name="reference_source"> + <param name="reference_source_selector" value="history" /> + <param name="database" value="mini-db.fa.gz" ftype="fasta.gz" /> + </conditional> + <param name="query" value="mini-query.fa.gz" ftype="fasta.gz"/> + <param name="minScore" value="0" /> + <section name="adv_align"> + <param name="stepSize" value="1"/> + </section> + <param name="out" value="psl" ftype="tabular" /> + <output name="output"> + <assert_contents> + <has_n_lines n="7"/> + </assert_contents> + </output> + <assert_command> + <has_text text="-minScore=0"/> + <has_text text="-stepSize=1"/> + </assert_command> + </test> </tests> <help> <![CDATA[ BLAT