Mercurial > repos > yating-l > ucsc_blat
comparison blat.xml @ 5:dede60f744f4 draft
planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7
| author | iuc |
|---|---|
| date | Fri, 23 Jun 2017 23:33:09 -0400 |
| parents | 545bc7831814 |
| children | 250a7f2b1331 |
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| 4:545bc7831814 | 5:dede60f744f4 |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="1.0"> | 2 <tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="35-0"> |
| 3 <description>Standalone blat sequence search command line tool</description> | 3 <description>BLAST-like sequence alignment tool</description> |
| 4 <requirements> | 4 <requirements> |
| 5 <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement> | 5 <requirement type="package" version="35">blat</requirement> |
| 6 </requirements> | 6 </requirements> |
| 7 <command detect_errors="exit_code"><![CDATA[ | 7 <command detect_errors="exit_code"><![CDATA[ |
| 8 #if str($reference_source.reference_source_selector) == "history": | 8 #if str($reference_source.reference_source_selector) == "history": |
| 9 #set $reference_fasta_filename = "localref.fa" | 9 ## blat depends on file extension |
| 10 #if $reference_source.database.is_of_type("fasta"): | |
| 11 #set $reference_fasta_filename = "localref.fa" | |
| 12 #elif $reference_source.database.is_of_type("twobit"): | |
| 13 #set $reference_fasta_filename = "localref.2bit" | |
| 14 #else | |
| 15 #set $reference_fasta_filename = "localref" | |
| 16 #end if | |
| 17 | |
| 10 ln -s '${reference_source.database}' '${reference_fasta_filename}' && | 18 ln -s '${reference_source.database}' '${reference_fasta_filename}' && |
| 11 #else: | 19 #else: |
| 12 #set $reference_fasta_filename = str($reference_source.database.fields.path) | 20 #set $reference_fasta_filename = str($reference_source.database.fields.path) |
| 13 #end if | 21 #end if |
| 22 | |
| 14 blat | 23 blat |
| 15 #if $noHead == "yes" | 24 #if $noHead == "yes" |
| 16 -noHead | 25 -noHead |
| 17 #end if | 26 #end if |
| 27 | |
| 18 -q=$query_type | 28 -q=$query_type |
| 19 -t=$database_type | 29 -t=$database_type |
| 30 | |
| 20 #if $mask_type.mask == "file.out": | 31 #if $mask_type.mask == "file.out": |
| 21 -mask=$mask_type.mask_file | 32 -mask='${mask_type.mask_file}' |
| 22 #else: | 33 #else: |
| 23 -mask=$mask_type.mask | 34 -mask=$mask_type.mask |
| 24 #end if | 35 #end if |
| 36 | |
| 25 '$reference_fasta_filename' | 37 '$reference_fasta_filename' |
| 26 '${query}' | 38 '${query}' |
| 39 | |
| 27 output | 40 output |
| 28 && sort -k 10,10 -k 12,12n output > '${output_sorted}' | 41 && sort -k 10,10 -k 12,12n output > '${output_sorted}' |
| 29 ]]></command> | 42 ]]></command> |
| 30 <inputs> | 43 <inputs> |
| 31 <conditional name="reference_source"> | 44 <conditional name="reference_source"> |
| 40 </options> | 53 </options> |
| 41 <validator type="no_options" message="A built-in database is not available" /> | 54 <validator type="no_options" message="A built-in database is not available" /> |
| 42 </param> | 55 </param> |
| 43 </when> | 56 </when> |
| 44 <when value="history"> | 57 <when value="history"> |
| 45 <param name="database" type="data" format="fasta,twobit" label="Using database file, either a .fa, .nib or .2bit file" /> | 58 <param name="database" type="data" format="fasta, twobit" label="Using database file, either a .fa, .nib or .2bit file" /> |
| 46 </when> | 59 </when> |
| 47 </conditional> | 60 </conditional> |
| 48 <param type="data" name="query" format="fasta,twobit" label="Query data, either a .fa, .nib or .2bit file"/> | 61 <param type="data" name="query" format="fasta, twobit" label="Query data, either a .fa, .nib or .2bit file"/> |
| 49 <param type="select" name="database_type" format="text" multiple="false" label="database type" help="Choose your database type, the default is dnax" argument="-t"> | 62 <param type="select" name="database_type" format="text" multiple="false" label="database type" help="Choose your database type, the default is dnax" argument="-t"> |
| 50 <option value="dna">dna - DNA sequence</option> | 63 <option value="dna">dna - DNA sequence</option> |
| 51 <option value="prot">prot - protein sequence</option> | 64 <option value="prot">prot - protein sequence</option> |
| 52 <option value="dnax" selected="true">dnax - DNA sequence translated in six frames to protein</option> | 65 <option value="dnax" selected="true">dnax - DNA sequence translated in six frames to protein</option> |
| 53 </param> | 66 </param> |