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changeset 5:f5a5a2b39ff2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 4568799de240022f4058ec1602e08f536916e2af"
author iuc
date Thu, 25 Mar 2021 20:53:27 +0000
parents 8705e0d74a0f
children 19c265784f35
files lastdb.xml macros_last.xml maf-convert.xml test-data/hedgdb.bck test-data/hedgdb.prj test-data/hedgdb.suf test-data/hedgdb.txt test-data/humdb-sanger.lastdb test-data/humdb-sanger.prj test-data/humdb.prj test-data/humdb.txt test-data/last_align_fastq.maf test-data/last_align_gen.maf test-data/last_align_prot.maf
diffstat 11 files changed, 143 insertions(+), 25 deletions(-) [+]
line wrap: on
line diff
--- a/lastdb.xml	Wed Mar 24 22:36:50 2021 +0000
+++ b/lastdb.xml	Thu Mar 25 20:53:27 2021 +0000
@@ -34,7 +34,9 @@
         -R $lastdb.repeats.uppercase$lastdb.repeats.simple_repeat 
         $lastdb.repeats.sm_lower 
         -S $lastdb.lastdb_advanced.S
-        -u $lastdb.lastdb_advanced.seeds.u
+        #if $lastdb.lastdb_advanced.seeds.u != ''
+            -u $lastdb.lastdb_advanced.seeds.u
+        #end if
         -w $lastdb.lastdb_advanced.seeds.w
         #if $lastdb.lastdb_advanced.seeds.W
             -W $lastdb.lastdb_advanced.seeds.W
@@ -90,7 +92,8 @@
                 </param>
 
                 <conditional name="seeds">
-                    <param argument="-u" type="select" multiple="false" optional="true" label="Specify a seeding scheme.">
+                    <param argument="-u" type="select" multiple="false" label="Specify a seeding scheme.">
+                        <option value="">Do not apply seeding scheme</option>
                         <option value="BISF">BISF</option>
                         <option value="BISR">BISR</option>
                         <option value="MAM4">MAM4</option>
@@ -100,6 +103,7 @@
                         <option value="YASS" selected="true">YASS</option>
                         <!-- Add filename option -->
                     </param>
+                    <when value=""/>
                     <when value="BISF">
                         <expand macro="step_macro" step="2"/>
                     </when>
@@ -171,6 +175,7 @@
             <section name="lastdb_advanced">
                 <conditional name="seeds">
                     <param name="u" value="MURPHY10"/>
+                </conditional>
             </section>
             <output name="outfile" compare="contains" file="hedgdb.lastdb" ftype="lastdb">
                 <extra_files type="file" value="hedgdb.bck" name="lastdb.bck" compare="sim_size" delta="1"/>
@@ -192,7 +197,7 @@
                     <param name="sm_lower" value="true"/>
                 </section>
             </section>
-            <output name="outfile" compare="contains" file="hedgdb.lastdb" ftype="lastdb">
+            <output name="outfile" compare="contains" file="humdb-sanger.lastdb" ftype="lastdb">
                 <extra_files type="file" value="humdb-sanger.bck" name="lastdb.bck" compare="sim_size" delta="1"/>
                 <extra_files type="file" value="humdb-sanger.des" name="lastdb.des"/>
                 <extra_files type="file" value="humdb-sanger.prj" name="lastdb.prj" lines_diff="2"/>
--- a/macros_last.xml	Wed Mar 24 22:36:50 2021 +0000
+++ b/macros_last.xml	Thu Mar 25 20:53:27 2021 +0000
@@ -36,7 +36,7 @@
                 </param>
             </when>
             <when value="lastdb">
-                <param name="lastdatabase" type="data" label="LAST database" />
+                <param name="lastdatabase" type="data" format="lastdb" label="LAST database" />
             </when>
         </conditional>
     </xml>
--- a/maf-convert.xml	Wed Mar 24 22:36:50 2021 +0000
+++ b/maf-convert.xml	Thu Mar 25 20:53:27 2021 +0000
@@ -59,9 +59,12 @@
                     <option value="sam">sam</option>
                     <option value="tab">tab</option>
                 </param>
+                <when value="axt"/>
                 <when value="blast">
                     <param argument="-l" type="integer" value="60" label="Line length"/>
                 </when>
+                <when value="blasttab"/>
+                <when value="chain"/>
                 <when value="html">
                     <param argument="-l" type="integer" value="60" label="Line length"/>
                 </when>
@@ -71,13 +74,18 @@
                 </when>
                 <when value="sam">
                     <conditional name="sam_file">
-                        <param name="dictionary" argument="-d" type="boolean" truevalue="-d" falsevalue="" checked="false" label="Include dictionary of sequence lengths in sam format"/>
+                        <param name="dictionary" argument="-d" type="select" label="Include dictionary of sequence lengths in sam format">
+                            <option value="-d">Yes</option>
+                            <option value="" selected="true">No</option>
+                        </param>
+                        <when value=""/>
                         <when value="-d">
                             <param argument="-f" type="data" format="dict" label="Get a sequence dictionary from DICTFILE" />
                         </when>
                     </conditional>			    
                     <param argument="-r" type="text" value="" label="Specify read group information" help="Example: 'ID:1 PL:ILLUMINA SM:mysample'"/>
                 </when>
+                <when value="tab"/>
             </conditional>
         </section>
     </inputs>
Binary file test-data/hedgdb.bck has changed
--- a/test-data/hedgdb.prj	Wed Mar 24 22:36:50 2021 +0000
+++ b/test-data/hedgdb.prj	Thu Mar 25 20:53:27 2021 +0000
@@ -1,4 +1,4 @@
-version=1021
+version=1205
 alphabet=ACDEFGHIKLMNPQRSTVWY
 numofsequences=1
 numofletters=411
@@ -10,17 +10,6 @@
 numofindexes=1
 integersize=32
 totallength=413
-specialcharacters=310
-prefixlength=2
-subsetseed=A C G T
-subsetseed=AG CT
-subsetseed=A C G T
-subsetseed=ACGT
-subsetseed=ACGT
-subsetseed=A C G T
-subsetseed=A C G T
-subsetseed=ACGT
-subsetseed=ACGT
-subsetseed=A C G T
-subsetseed=ACGT
-subsetseed=A C G T
+specialcharacters=2
+prefixlength=1
+subsetseed=ILMV FWY A C G H P KR ST DENQ
Binary file test-data/hedgdb.suf has changed
--- a/test-data/humdb-sanger.prj	Wed Mar 24 22:36:50 2021 +0000
+++ b/test-data/humdb-sanger.prj	Thu Mar 25 20:53:27 2021 +0000
@@ -1,4 +1,4 @@
-version=1021
+version=1205
 alphabet=ACGT
 numofsequences=1
 numofletters=16571
--- a/test-data/humdb.prj	Wed Mar 24 22:36:50 2021 +0000
+++ b/test-data/humdb.prj	Thu Mar 25 20:53:27 2021 +0000
@@ -1,4 +1,4 @@
-version=1021
+version=1205
 alphabet=ACGT
 numofsequences=1
 numofletters=16571
--- a/test-data/last_align_fastq.maf	Wed Mar 24 22:36:50 2021 +0000
+++ b/test-data/last_align_fastq.maf	Thu Mar 25 20:53:27 2021 +0000
@@ -2,7 +2,7 @@
 #
 # a=7 b=1 A=7 B=1 e=22 d=13 x=21 y=9 z=21 D=1e+06
 # R=10 u=0 s=2 S=0 M=0 T=0 m=10 l=1 L=999999999 n=10 k=1 w=1000 t=2.82533 j=3 Q=1
-# /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb-sanger
+# /home/berntm/.planemo/planemo_tmp_vt3pko3h/test-data/humdb-sanger
 # Reference sequences=1 normal letters=16571
 #
 #    A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  J  Z  X  *
--- a/test-data/last_align_gen.maf	Wed Mar 24 22:36:50 2021 +0000
+++ b/test-data/last_align_gen.maf	Thu Mar 25 20:53:27 2021 +0000
@@ -2,7 +2,7 @@
 #
 # a=7 b=1 A=7 B=1 e=22 d=13 x=21 y=9 z=21 D=1e+06
 # R=10 u=0 s=2 S=0 M=0 T=0 m=10 l=1 L=999999999 n=10 k=1 w=1000 t=2.82533 j=3 Q=0
-# /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb
+# /home/berntm/.planemo/planemo_tmp_vt3pko3h/test-data/humdb
 # Reference sequences=1 normal letters=16571
 #
 #    A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  J  Z  X  *
--- a/test-data/last_align_prot.maf	Wed Mar 24 22:36:50 2021 +0000
+++ b/test-data/last_align_prot.maf	Thu Mar 25 20:53:27 2021 +0000
@@ -2,7 +2,7 @@
 #
 # a=11 b=2 A=11 B=2 e=22 d=13 x=21 y=9 z=21 D=1e+06 E=2.73494e+09
 # R=10 u=0 s=1 S=0 M=0 T=0 m=10 l=1 L=999999999 n=10 k=1 w=1000 t=3.08611 j=3 Q=0
-# /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/hedgdb
+# /home/berntm/.planemo/planemo_tmp_vt3pko3h/test-data/hedgdb
 # Reference sequences=1 normal letters=411
 # lambda=0.305935 K=0.102404
 #
@@ -39,4 +39,120 @@
 # name start alnSize strand seqSize alignment
 #
 # batch 0
+a score=729 EG2=1.4e-80 E=1.2e-101
+s NP_002172.2    13 264 + 411 LVLLLLLVVPA----AWGCGPGRVVGSRRRPPRKLVPLAYKQFSPNVPEKTLGASGRYEGKIARSSERFKELTPNYNPDIIFKDEENTGADRLMTQRCKDRLNSLAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDITTSDRDRNKYGLLARLAVEAGFDWVYYESKAHVHCSVKSEHSAAAKTGGCFPAGAQVRLESGARVALSAVRPGDRVLAMGEDGSPTFSDVLIFLDREPHRLRAFQVIETQDPPRRLALTPAHLL
+s NP_001034065.1 66 265 + 471 LVALLLIVLPMVFSPAHSCGPGRGLGRHRA--RNLYPLVLKQTIPNLSEYTNSASGPLEGVIRRDSPKFKDLVPNYNRDILFRDEEGTGADRLMSKRCKEKLNVLAYSVMNEWPGIRLLVTESWDEDYHHGQESLHYEGRAVTIATSDRDQSKYGMLARLAVEAGFDWVSYVSRRHIYCSVKSDSSISSHVHGCFTPESTALLESGVRKPLGELSIGDRVLSMTANGQAVYSEVILFMDRNLEQMQNFVQLHT-DGGAVLTVTPAHLV
+
+a score=131 EG2=0.4 E=4.1e-14
+s NP_002172.2    293 95 + 411 FASHVQPGQYVLVAGVPG--LQPARVAAVSTHVALGAYAPLTKHGTLVVEDVVASCFAAVADHHLAQLAFWPLRLFHSLAWGSWTPG-EGVHWYPQLL
+s NP_001034065.1 344 96 + 471 FADRIEEKNQVLVRDVETGELRPQRVVKVGSVRSKGVVAPLTREGTIVVNSVAASCYAVINSQSLAHWGLAPMRLLSTLE--AWLPAKEQLHSSPKVV
+
+a score=50 EG2=2.3e+10 E=0.0037
+s NP_002172.2    379 23 + 411 GVHWYPQLLYRLGRLLLEEGSFH
+s NP_001034065.1 447 23 + 471 GIHWYANALYKVKDYVLPQSWRH
+
+a score=41 EG2=3.7e+11 E=0.06
+s NP_002172.2    91 34 + 411 KDEENTGADRLMTQRCKDRLNSLAISVMNQWPGV
+s NP_001034065.1 44 34 + 471 QEETQTMRHIAHTQRCLSRLTSLVALLLIVLPMV
+
+a score=32 EG2=5.7e+12 E=0.99
+s NP_002172.2    183 24 + 411 AHVHCSVKSEHSAAAKTGGCFPAG
+s NP_001034065.1 252 24 + 471 SHVHGCFTPESTALLESGVRKPLG
+
+a score=31 EG2=7.8e+12 E=1.3
+s NP_002172.2    146 21 + 411 EGRAVDITTSDRDRNKYGLLA
+s NP_001034065.1 149 21 + 471 EGTGADRLMSKRCKEKLNVLA
+
+a score=31 EG2=7.8e+12 E=1.3
+s NP_002172.2    394 16 + 411 LLEEGSFHPLGMSGAG
+s NP_001034065.1 265 16 + 471 LLESGVRKPLGELSIG
+
+a score=30 EG2=1.1e+13 E=1.8
+s NP_002172.2     23 13 + 411 AAWGCGPGRVVGS
+s NP_001034065.1 409 13 + 471 AHWGLAPMRLLST
+
+a score=30 EG2=1.1e+13 E=1.8
+s NP_002172.2    180 18 + 411 ESKAHVHCSVKSEHSAAA
+s NP_001034065.1  20 18 + 471 DAKCHSSSSSSSSKSAAS
+
+a score=28 EG2=2e+13 E=3.4
+s NP_002172.2    167 20 + 411 RLAVEAGFDWVYYESKAHVH
+s NP_001034065.1 180 20 + 471 RLLVTESWDEDYHHGQESLH
+
+a score=28 EG2=2e+13 E=3.4
+s NP_002172.2    181 20 + 411 SKAHVHCSVKSEHSAAAKTG
+s NP_001034065.1 428 20 + 471 AKEQLHSSPKVVSSAQQQNG
+
+a score=26 EG2=3.6e+13 E=6.4
+s NP_002172.2    233 17 + 411 EDGSPTFSDVLIFLDRE
+s NP_001034065.1 133 17 + 471 KDLVPNYNRDILFRDEE
+
+a score=25 EG2=4.9e+13 E=8.7
+s NP_002172.2    236 14 + 411 SPTFSDVLIFLDRE
+s NP_001034065.1 129 14 + 471 SPKFKDLVPNYNRD
+
+a score=24 EG2=6.6e+13 E=12
+s NP_002172.2     10 16 + 411 HFCLVLLLLLVVPAAW
+s NP_001034065.1 410 16 + 471 HWGLAPMRLLSTLEAW
+
+a score=24 EG2=6.6e+13 E=12
+s NP_002172.2     26 23 + 411 GCGPGRVVGSRRRPPRKLVPLAY
+s NP_001034065.1 150 21 + 471 GTGADRLMSKRCK--EKLNVLAY
+
+a score=24 EG2=6.6e+13 E=12
+s NP_002172.2     48 32 + 411 YKQFSPNVPEKTLGASGRYEGKIARSSERFKE
+s NP_001034065.1 132 32 + 471 FKDLVPNYNRDILFRDEEGTGADRLMSKRCKE
+
+a score=24 EG2=6.6e+13 E=12
+s NP_002172.2    106 27 + 411 CKDRLNSLAISVMNQWPGVKLRVTEGW
+s NP_001034065.1 399 27 + 471 CYAVINSQSLAHWGLAPMRLLSTLEAW
+
+a score=24 EG2=6.6e+13 E=12
+s NP_002172.2    143 8 + 411 LHYEGRAV
+s NP_001034065.1 314 8 + 471 LHTDGGAV
+
+a score=24 EG2=6.6e+13 E=12
+s NP_002172.2    157 14 + 411 RDRNKYGLLARLAV
+s NP_001034065.1  94 14 + 471 RARNLYPLVLKQTI
+
+a score=23 EG2=9e+13 E=16
+s NP_002172.2     20 6 + 411 VVPAAW
+s NP_001034065.1 462 6 + 471 VLPQSW
+
+a score=23 EG2=9e+13 E=16
+s NP_002172.2    146 22 + 411 EGRAVDITTSDRDRNKYGLLAR
+s NP_001034065.1 336 22 + 471 ESQKLTFVFADRIEEKNQVLVR
+
+a score=23 EG2=9e+13 E=16
+s NP_002172.2    173 11 + 411 GFDWVYYESKA
+s NP_001034065.1 194 11 + 471 GQESLHYEGRA
+
+a score=23 EG2=9e+13 E=16
+s NP_002172.2    207 15 + 411 AQVRLESGARVALSA
+s NP_001034065.1 428 15 + 471 AKEQLHSSPKVVSSA
+
+a score=23 EG2=9e+13 E=16
+s NP_002172.2    317 14 + 411 AAVSTHVALGAYAP
+s NP_001034065.1 248 13 + 471 SSISSHVH-GCFTP
+
+a score=23 EG2=9e+13 E=16
+s NP_002172.2    331 13 + 411 LTKHGTLVVEDVV
+s NP_001034065.1 286 13 + 471 MTANGQAVYSEVI
+
+a score=23 EG2=9e+13 E=16
+s NP_002172.2    361 11 + 411 WP-LRLFHSLAW
+s NP_001034065.1 176 12 + 471 WPGIRLLVTESW
+
+a score=22 EG2=1.2e+14 E=22
+s NP_002172.2    264 22 + 411 PPRRLALTPAHLLFTADNHTEP
+s NP_001034065.1 415 22 + 471 PMRLLSTLEAWLPAKEQLHSSP
+
+a score=22 EG2=1.2e+14 E=22
+s NP_002172.2    268 7 + 411 LALTPAH
+s NP_001034065.1  76 7 + 471 MVFSPAH
+
+a score=22 EG2=1.2e+14 E=22
+s NP_002172.2    277 21 + 411 FTADNHTEPAARFRATFASHV
+s NP_001034065.1 234 21 + 471 YVSRRHIYCSVKSDSSISSHV
+
 # Query sequences=1