Mercurial > repos > yating-l > ucsc_blat

changeset 7:10f3a5b6f2ac draft

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planemo upload commit 964ceec6b1c6371b10923c7d49446b1361fc5895-dirty
author yating-l
date Mon, 09 Jul 2018 13:07:54 -0400
parents 250a7f2b1331
children 7532cec01999
files README.rst blat.xml datatypes_conf.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/amaVit1_Gallus/amaVit1_Gallus_gallus_sorted.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
diffstat 6 files changed, 260 insertions(+), 310 deletions(-) [+]
line wrap: on
line diff
--- 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml	Mon Jul 09 13:07:54 2018 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<datatypes>
+  <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications">
+    <datatype extension="psl" subclass="True" type="galaxy.datatypes.tabular:Tabular" />
+  </registration>
+</datatypes>
\ No newline at end of file
--- a/test-data/amaVit1_Gallus/amaVit1_Gallus_gallus_sorted.psl	Thu May 31 11:25:53 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-1247	370	0	44	6	280	17	96639	+-	NM_001012804	4592	121	2062	LMAW01000001.1	10443977	517465	615765	18	119,32,74,112,2,87,150,114,39,171,3,94,58,142,81,107,137,139,	121,240,272,355,467,469,598,757,1066,1129,1300,1303,1397,1455,1597,1679,1786,1923,	9828212,9828431,9869264,9881475,9881600,9882641,9893172,9893708,9899022,9904744,9904997,9908755,9909749,9911745,9915154,9915481,9920844,9926373,
-143	58	0	19	3	659	4	9089	++	NM_204766	5992	574	1453	LMAW01000003.1	4188689	259524	268833	5	27,80,11,66,36,	574,700,780,847,1417,	259524,261255,261529,262379,268797,
-182	48	0	20	1	24	0	0	+-	NM_001292086	6644	508	782	LMAW01000003.1	4188689	2832901	2833151	2	102,148,	508,634,	1355538,1355640,
-189	73	0	0	4	773	4	13674	++	NM_204766	5992	553	1588	LMAW01000003.1	4188689	2559457	2573393	5	84,66,33,13,66,	553,739,844,1457,1522,	2559457,2563244,2563349,2570767,2573327,
-200	50	0	0	0	0	1	24	+-	NM_001292086	6644	481	731	LMAW01000003.1	4188689	2832850	2833124	2	110,140,	481,591,	1355565,1355699,
-2134	377	0	62	6	361	28	33978	++	NM_001006176	3248	296	3230	LMAW01000001.1	10443977	10027590	10064141	29	110,48,10,76,75,152,66,51,87,83,55,56,148,96,63,24,177,107,83,145,109,83,145,90,117,129,68,93,27,	296,406,454,502,578,653,844,910,961,1048,1131,1186,1242,1390,1486,1609,1741,1918,2025,2108,2253,2362,2445,2590,2680,2797,2926,3034,3203,	10027590,10031154,10031353,10031517,10033261,10033696,10034454,10035646,10043484,10043794,10059668,10059824,10059973,10060798,10060979,10061265,10061487,10061740,10061947,10062143,10062365,10062584,10062743,10063001,10063188,10063383,10063616,10063806,10064114,
-2710	404	0	198	24	2053	34	11593	+-	NM_001292086	6644	10	5375	LMAW01000003.1	4188689	2820233	2835138	37	64,727,107,5,90,146,87,93,135,137,171,93,72,90,69,90,23,34,9,72,125,70,106,21,23,161,26,29,93,15,45,18,11,12,54,162,27,	10,74,801,908,913,1003,1149,1236,1329,1464,1617,1792,1885,2049,2163,2350,2918,3036,3070,3366,3445,3576,3647,3794,3985,4008,4236,4263,4476,4603,4688,4742,4882,4941,5031,5113,5348,	1353551,1355131,1356116,1356798,1356971,1357445,1359020,1359444,1359816,1360523,1360971,1361443,1365082,1365245,1365351,1365525,1366096,1366220,1366255,1366474,1366549,1366674,1366749,1366889,1367081,1367105,1367332,1367358,1367558,1367688,1367786,1367837,1367979,1368029,1368113,1368194,1368429,
-3724	1107	0	326	14	609	44	22663	++	NM_204766	5992	49	5815	LMAW01000002.1	5883884	103604	131424	45	51,78,132,3,152,2,29,75,90,63,1,95,81,3,136,119,150,2,169,180,123,48,90,117,123,134,241,261,177,146,90,72,267,129,81,2,196,348,116,193,106,123,177,99,87,	49,154,256,388,391,543,545,574,691,781,844,845,967,1048,1051,1187,1306,1456,1458,1627,1807,1960,2008,2098,2215,2338,2472,2713,2974,3151,3298,3388,3493,3778,3943,4024,4026,4222,4696,4812,5051,5212,5335,5608,5728,	103604,104407,107764,107909,108002,108233,108257,109261,112047,112967,113036,113148,114257,114391,114866,116183,116438,116593,116908,117767,118030,118682,120119,120672,121329,122185,122724,123518,123945,124449,124904,125793,125898,126790,127405,127543,127717,128055,129238,129442,129761,130020,130254,131103,131337,
-420	114	0	0	4	99	3	7093	++	NM_001031013	971	69	702	LMAW01000002.1	5883884	3610886	3618513	5	33,66,21,276,138,	69,138,232,285,564,	3610886,3610955,3617941,3618099,3618375,
-49	11	0	0	0	0	0	0	+-	NM_001292086	6644	619	679	LMAW01000003.1	4188689	2833085	2833145	1	60,	619,	1355544,
-537	234	0	42	7	1113	7	34987	++	NM_204766	5992	262	2188	LMAW01000001.1	10443977	9729332	9765132	8	108,153,66,93,39,171,99,84,	262,388,574,688,1414,1459,1981,2104,	9729332,9734141,9751019,9755220,9762042,9762555,9764665,9765048,
-92	25	0	0	0	0	1	183	+-	NM_001292086	6644	562	679	LMAW01000003.1	4188689	2832851	2833151	2	43,74,	562,605,	1355538,1355764,
--- a/test-data/dbia3/dbia3.sorted.psl	Thu May 31 11:25:53 2018 -0400
+++ b/test-data/dbia3/dbia3.sorted.psl	Mon Jul 09 13:07:54 2018 -0400
@@ -1,147 +1,147 @@
 46	8	0	0	0	0	0	0	++	FBtr0070000	3537	2966	3020	contig55	40015	26192	26246	1	54,	2966,	26192,
-46	8	0	0	0	0	0	0	++	FBtr0307554	3546	2975	3029	contig55	40015	26192	26246	1	54,	2975,	26192,
-46	8	0	0	0	0	0	0	++	FBtr0307555	4528	3113	3167	contig55	40015	26192	26246	1	54,	3113,	26192,
-39	9	0	0	0	0	0	0	++	FBtr0070075	2430	1838	1886	contig65	45013	12112	12160	1	48,	1838,	12112,
-39	9	0	0	0	0	0	0	++	FBtr0070075	2430	1838	1886	contig64	40016	32121	32169	1	48,	1838,	32121,
+50	10	0	0	0	0	0	0	+-	FBtr0070075	2430	1826	1886	contig67	44531	31857	31917	1	60,	1826,	12614,
+38	7	0	0	0	0	0	0	+-	FBtr0070075	2430	1838	1883	contig10	43013	28990	29035	1	45,	1838,	13978,
+38	7	0	0	0	0	0	0	+-	FBtr0070075	2430	1838	1883	contig11	35013	7985	8030	1	45,	1838,	26983,
+38	7	0	0	0	0	0	0	+-	FBtr0070075	2430	1838	1883	contig23	50012	49307	49352	1	45,	1838,	660,
+38	7	0	0	0	0	0	0	+-	FBtr0070075	2430	1838	1883	contig24	40010	29304	29349	1	45,	1838,	10661,
+38	7	0	0	0	0	0	0	+-	FBtr0070075	2430	1838	1883	contig25	75023	20928	20973	1	45,	1838,	54050,
+38	7	0	0	0	0	0	0	+-	FBtr0070075	2430	1838	1883	contig30	70018	55814	55859	1	45,	1838,	14159,
+38	7	0	0	0	0	0	0	+-	FBtr0070075	2430	1838	1883	contig31	40012	15807	15852	1	45,	1838,	24160,
+38	7	0	0	0	0	0	0	+-	FBtr0070075	2430	1838	1883	contig35	48011	33007	33052	1	45,	1838,	14959,
+38	7	0	0	0	0	0	0	+-	FBtr0070075	2430	1838	1883	contig36	45010	8000	8045	1	45,	1838,	36965,
+38	7	0	0	0	0	0	0	+-	FBtr0070075	2430	1838	1883	contig50	40009	19266	19311	1	45,	1838,	20698,
+38	7	0	0	0	0	0	0	+-	FBtr0070075	2430	1838	1883	contig51	50015	4265	4310	1	45,	1838,	45705,
+39	9	0	0	0	0	0	0	++	FBtr0070075	2430	1838	1886	contig12	56019	44985	45033	1	48,	1838,	44985,
+39	9	0	0	0	0	0	0	+-	FBtr0070075	2430	1838	1886	contig13	45015	38726	38774	1	48,	1838,	6241,
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--- a/test-data/dbia3/dbia3_masked.sorted.psl	Thu May 31 11:25:53 2018 -0400
+++ b/test-data/dbia3/dbia3_masked.sorted.psl	Mon Jul 09 13:07:54 2018 -0400
@@ -1,61 +1,61 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Jul 09 13:07:54 2018 -0400
@@ -0,0 +1,27 @@
+<?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