Mercurial > repos > yating-l > ucsc_blat
diff blat.xml @ 7:10f3a5b6f2ac draft
planemo upload commit 964ceec6b1c6371b10923c7d49446b1361fc5895-dirty
author | yating-l |
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date | Mon, 09 Jul 2018 13:07:54 -0400 |
parents | 250a7f2b1331 |
children | a9d863528f48 |
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--- a/blat.xml Thu May 31 11:25:53 2018 -0400 +++ b/blat.xml Mon Jul 09 13:07:54 2018 -0400 @@ -1,70 +1,31 @@ <?xml version="1.0"?> -<tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="36"> - <description>BLAST-like sequence alignment tool</description> +<tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="1.1"> + <description>Standalone blat sequence search command line tool</description> <requirements> - <requirement type="package" version="36">blat</requirement> + <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement> </requirements> <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"): - #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 - + #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 - + blat + #if $noHead == "yes" + -noHead + #end if -q=$query_type -t=$database_type - - ${oneOff} - - #if str($minScore) - -minScore=${minScore} - #end if - - -maxGap=${maxGap} - - #if str($repMatch) - -repMatch=${repMatch} - #end if - #if $mask_type.mask == "file.out": - -mask='${mask_type.mask_file}' + -mask=$mask_type.mask_file #else: -mask=$mask_type.mask #end if - - #if str($dots) - -dots=${dots} - #end if - - ${trimT} - ${noTrimA} - ${trimHardA} - ${fastMap} - ${fine} - - #if str($maxIntron) - -maxIntron=${maxIntron} - #end if - - ${extendThroughN} - '$reference_fasta_filename' '${query}' - - -out=${out} - - '${output}' + output + && sort -k 10,10 -k 12,12n output > '${output_sorted}' ]]></command> <inputs> <conditional name="reference_source"> @@ -81,10 +42,10 @@ </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> @@ -97,10 +58,10 @@ <option value="dnax">dnax - DNA sequence translated in six frames to protein</option> <option value="rnax" selected="true">rnax - DNA sequence translated in three frames to protein</option> </param> - <param argument="-oneOff" type="boolean" truevalue="-oneOff=1" falsevalue="" label="If set, this allows one mismatch in tile and still triggers an alignments" /> - <param argument="-minScore" type="integer" value="30" label="Minimum score" help="It is the matches minus the mismatches minus some sort of gap penalty" /> - <param argument="-maxGap" type="integer" value="2" min="0" max="3" label="Maximum gap between tiles in a clump" help="Usually set from 0 to 3. Only relevant for minMatch > 1" /> - <param argument="-repMatch" type="integer" value="" optional="true" label="Number of repetitions of a tile allowed before it is marked as overused" help="Typically this is 256 for tileSize 12, 1024 for tileSize 11, 4096 for tileSize 10. Also affected by stepSize. When stepSize is halved repMatch is doubled to compensate" /> + <param type="select" name="noHead" format="text" label="Suppresses .psl header (so it's just a tab-separated file)." > + <option value="yes" selected="true">Yes, suppresses .psl header</option> + <option value="no">No, do not suppresses .psl header</option> + </param> <conditional name="mask_type"> <param name="mask" type="select" label="Mask out repeats" help="Alignments won't be started in masked region but may extend through it in nucleotide searches. Masked areas @@ -115,39 +76,11 @@ <when value="out" /> <when value="file.out"> <param name="mask_file" type="data" format="txt" label="RepeatMasker file.out" /> - </when> + </when> </conditional> - <param argument="-dots" type="integer" value="" optional="true" label="Output a dot every N sequences in log" help="Dots show program's progress" /> - <param argument="-trimT" type="boolean" truevalue="-trimT" falsevalue="" label="Trim leading poly-T" /> - <param argument="-noTrimA" type="boolean" truevalue="-noTrimA" falsevalue="" label="Don't trim trailing poly-A" /> - <param argument="-trimHardA" type="boolean" truevalue="-trimHardA" falsevalue="" label="Remove poly-A tail from qSize and alignments in .psl output" /> - <param argument="-fastMap" type="boolean" truevalue="-fastMap" falsevalue="" label="Run for fast DNA/DNA remapping" help="It does not allow introns and require high %ID. Query sizes must not exceed 5000" /> - <param argument="-fine" type="boolean" truevalue="-fine" falsevalue="" label="Refine search for small initial and terminal exons" help="For high-quality mRNAs. Not recommended for ESTs" /> - <param argument="-maxIntron" type="integer" value="750000" optional="true" label="Maximum intron size" /> - <param argument="-extendThroughN" type="boolean" truevalue="-extendThroughN" falsevalue="" label="Allow extension of alignment through large blocks of N's" /> - <param name="out" type="select" label="Select output file format (-out)"> - <option value="psl">Tab-separated format, no sequence (psl)</option> - <option value="psl -noHead">Tab-separated format, no sequence, no header (psl -noHead)</option> - <option value="axt">Blastz-associated axt format (axt)</option> - <option value="maf">Multiz-associated maf format (maf)</option> - <option value="sim4">Similar to sim4 format (sim4)</option> - <option value="wublast">Similar to WU-BLAST format (wublast)</option> - <option value="blast">Similar to NCBI BLAST format (blast)</option> - <option value="blast8">NCBI BLAST tabular format (blast8)</option> - <option value="blast9">NCBI BLAST tabular format with comments (blast9)</option> - </param> </inputs> <outputs> - <data name="output" format="tabular" label="${tool.name} on ${on_string}"> - <change_format> - <when input="out" value="psl" format="psl" /> - <when input="out" value="axt" format="axt" /> - <when input="out" value="maf" format="maf" /> - <when input="out" value="sim4" format="txt" /> - <when input="out" value="wublast" format="txt" /> - <when input="out" value="blast" format="txt" /> - </change_format> - </data> + <data format="psl" name="output_sorted" label="${tool.name} on ${on_string}"></data> </outputs> <tests> <!-- test on query of GenBank RefSeq records for Gallus gallus and database of Amazona vittata --> @@ -155,53 +88,44 @@ <param name="reference_source_selector" value="history" /> <param name="database" value="amaVit1_Gallus/amaVit1.fa" /> <param name="query" value="amaVit1_Gallus/Gallus_gallus_RefSeq.fa" /> - <param name="database_type" value="dnax" /> - <param name="query_type" value="rnax" /> + <param name="database_type" value="dnax" /> + <param name="query_type" value="rnax" /> + <param name="noHead" value="yes" /> <param name="mask" value="lower" /> - <param name="out" value="psl -noHead" /> - <output name="output" value="amaVit1_Gallus/amaVit1_Gallus_gallus_sorted.psl" sort="True"/> + <output name="output_sorted" value="amaVit1_Gallus/amaVit1_Gallus_gallus.psl" /> </test> <!-- test on query of partial mRNA of Drosophila melanogaster and the database of Drosophila biamipes dot chromosome --> <test> <param name="reference_source_selector" value="history" /> <param name="database" value="dbia3/dbia3.fa" /> <param name="query" value="dbia3/dmel-transcript.fa" /> - <param name="database_type" value="dnax" /> - <param name="query_type" value="rnax" /> + <param name="database_type" value="dnax" /> + <param name="query_type" value="rnax" /> + <param name="noHead" value="yes" /> <param name="mask" value="lower" /> - <param name="out" value="psl -noHead" /> - <param name="maxIntron" value="" /> - <output name="output" value="dbia3/dbia3.sorted.psl" sort="True"/> + <output name="output_sorted" value="dbia3/dbia3.sorted.psl" /> </test> <!-- test on the database masked by repeat masker --> <test> <param name="reference_source_selector" value="history" /> <param name="database" value="dbia3/dbia3_masked.2bit" /> <param name="query" value="dbia3/dmel-transcript.fa" /> - <param name="database_type" value="dnax" /> - <param name="query_type" value="rnax" /> - <param name="oneOff" value="false" /> - <param name="minScore" value="30" /> - <param name="maxGap" value="2" /> - <param name="trimT" value="false" /> - <param name="noTrimA" value="false" /> - <param name="fine" value="false" /> - <param name="maxIntron" value="750000" /> - <param name="extendThroughN" value="false" /> + <param name="database_type" value="dnax" /> + <param name="query_type" value="rnax" /> + <param name="noHead" value="yes" /> <param name="mask" value="file.out" /> <param name="mask_file" value="dbia3/dbia3_RM.out" /> - <param name="out" value="psl -noHead" /> - <output name="output" value="dbia3/dbia3_masked.sorted.psl"/> + <output name="output_sorted" value="dbia3/dbia3_masked.sorted.psl" /> </test> - </tests> + </tests> <help> <![CDATA[ BLAT ==== -BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments. +BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments. -blat (version: v36)- Standalone blat sequence search command line tool. +blat (version: v340)- Standalone blat sequence search command line tool. ------------------------------------------------------------------------- usage: @@ -215,20 +139,25 @@ -ooc=11.ooc tells the program to load over-occurring 11-mers from an external file. This will increase the speed by a factor of 40 in many cases, but is not required. - output.psl is the name of the output file. + output.psl is the name of the output file. documentation: ++++++++++++++ -See Blat documentation (http://genome.ucsc.edu/goldenPath/help/blatSpec.html) +See Blat documentation (http://genome.ucsc.edu/goldenPath/help/blatSpec.html) Source code: ++++++++++++ http://hgdownload.cse.ucsc.edu/admin/exe/ -]]></help> +]]></help> <citations> <citation type="doi">10.1101/gr.229202</citation> -</citations> +</citations> </tool> + + + + + \ No newline at end of file