Mercurial > repos > yating-l > ucsc_blat
changeset 19:355af6f61974 draft
planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df-dirty
author | yating-l |
---|---|
date | Fri, 12 May 2017 17:22:07 -0400 |
parents | 275949b792a4 |
children | 181a8b8ac4da |
files | blat.xml test-data/all_fasta.loc |
diffstat | 2 files changed, 57 insertions(+), 16 deletions(-) [+] |
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--- a/blat.xml Fri May 12 15:52:39 2017 -0400 +++ b/blat.xml Fri May 12 17:22:07 2017 -0400 @@ -5,23 +5,23 @@ <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - #set $reference_fasta_filename = "localref.fa" - #if str($reference_source.reference_source_selector) == "history": - ln -s '${reference_source.database}' '${reference_fasta_filename}' - #else: + #if str($reference_source.reference_source_selector) == "history": + #set $reference_fasta_filename = "localref.fa" + ln -s '${reference_source.database}' '${reference_fasta_filename}' && + #else: #set $reference_fasta_filename = str($reference_source.database.fields.path) - #end if - && blat - #if $noHead == "yes" - -noHead - #end if - -q=$query_type - -t=$database_type - -mask=$mask - '${reference_fasta_filename}' - '${query}' - output - && sort -k 10,10 -k 12,12n output > '${output_sorted}' + #end if + blat + #if $noHead == "yes" + -noHead + #end if + -q=$query_type + -t=$database_type + -mask=$mask + '$reference_fasta_filename' + '${query}' + output + && sort -k 10,10 -k 12,12n output > '${output_sorted}' ]]></command> <inputs> <conditional name="reference_source"> @@ -32,6 +32,7 @@ <when value="cached"> <param name="database" type="select" label="Select database"> <options from_data_table="all_fasta"> + <filter type="sort_by" column="2" /> </options> <validator type="no_options" message="A built-in database is not available" /> </param> @@ -90,6 +91,16 @@ <param name="mask" value="lower" /> <output name="output_sorted" value="dbia3/dbia3.sorted.psl" /> </test> + <test> + <param name="reference_source_selector" value="cached" /> + <param name="database" value="dbia3" /> + <param name="query" value="dbia3/dmel-all-transcript-r6.13.fasta" /> + <param name="database_type" value="dnax" /> + <param name="query_type" value="rnax" /> + <param name="noHead" value="yes" /> + <param name="mask" value="lower" /> + <output name="output_sorted" value="dbia3/dbia3.sorted.psl" /> + </test> </tests> <help>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Fri May 12 17:22:07 2017 -0400 @@ -0,0 +1,30 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa +dbia3 dm3 Dbia3 /home/galaxy/galaxy/tool-data/dm3/seq/dbia3.fa \ No newline at end of file