Mercurial > repos > yating-l > ucsc_blat
changeset 5:dede60f744f4 draft
planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7
author | iuc |
---|---|
date | Fri, 23 Jun 2017 23:33:09 -0400 |
parents | 545bc7831814 |
children | 250a7f2b1331 |
files | README.rst blat.xml test-data/all_fasta.loc test-data/amaVit1_Gallus/Gallus_gallus_RefSeq.fa test-data/amaVit1_Gallus/amaVit1.fa test-data/amaVit1_Gallus/amaVit1_Gallus_gallus.psl test-data/amaVit1_Gallus/amaVit1_Gallus_gallus_filtered.psl test-data/dbia3/dbia3.fa test-data/dbia3/dbia3.sorted.psl test-data/dbia3/dbia3_RM.out test-data/dbia3/dbia3_masked.2bit test-data/dbia3/dbia3_masked.sorted.psl test-data/dbia3/dmel-transcript.fa tool-data/all_fasta.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml tools/ucsc_blat/.gitignore |
diffstat | 3 files changed, 22 insertions(+), 40 deletions(-) [+] |
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--- a/blat.xml Thu Jun 01 16:31:08 2017 -0400 +++ b/blat.xml Fri Jun 23 23:33:09 2017 -0400 @@ -1,29 +1,42 @@ <?xml version="1.0"?> -<tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="1.0"> - <description>Standalone blat sequence search command line tool</description> +<tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="35-0"> + <description>BLAST-like sequence alignment tool</description> <requirements> - <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement> + <requirement type="package" version="35">blat</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ #if str($reference_source.reference_source_selector) == "history": - #set $reference_fasta_filename = "localref.fa" + ## blat depends on file extension + #if $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" + #else + #set $reference_fasta_filename = "localref" + #end if + ln -s '${reference_source.database}' '${reference_fasta_filename}' && #else: #set $reference_fasta_filename = str($reference_source.database.fields.path) #end if + blat #if $noHead == "yes" - -noHead + -noHead #end if + -q=$query_type -t=$database_type + #if $mask_type.mask == "file.out": - -mask=$mask_type.mask_file + -mask='${mask_type.mask_file}' #else: -mask=$mask_type.mask #end if + '$reference_fasta_filename' '${query}' + output && sort -k 10,10 -k 12,12n output > '${output_sorted}' ]]></command> @@ -42,10 +55,10 @@ </param> </when> <when value="history"> - <param name="database" type="data" format="fasta,twobit" label="Using database file, either a .fa, .nib or .2bit file" /> + <param name="database" type="data" format="fasta, twobit" label="Using database file, either a .fa, .nib or .2bit file" /> </when> </conditional> - <param type="data" name="query" format="fasta,twobit" label="Query data, either a .fa, .nib or .2bit file"/> + <param type="data" name="query" format="fasta, twobit" label="Query data, either a .fa, .nib or .2bit file"/> <param type="select" name="database_type" format="text" multiple="false" label="database type" help="Choose your database type, the default is dnax" argument="-t"> <option value="dna">dna - DNA sequence</option> <option value="prot">prot - protein sequence</option> @@ -160,4 +173,4 @@ - \ No newline at end of file +
--- a/tool_dependencies.xml Thu Jun 01 16:31:08 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <!-- required tools: - - blat - - sort - - pslReps - - faPolyASizes - - pslCDnaFilter - --> - <package name="ucsc_tools_340_for_BLAT" version="1.0"> - <install version="1.0"> - <actions_group> - <actions architecture="x86_64" os="linux"> - <action type="download_by_url">http://old-gep.wustl.edu/~galaxy/package_ucsc_tools_340_for_BLAT.tar.gz</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR/bin</destination_directory> - </action> - </actions> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions_group> - </install> - <readme>The tools and utilities were created by the UCSC Genome Bioinformatics Group</readme> - </package> -</tool_dependency> \ No newline at end of file