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changeset 3:ebd03dc31ed4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 32693b6ea0a12cd77294fdc3cae53863cba4a8f6
author iuc
date Wed, 26 Aug 2015 08:11:49 -0400
parents 90759bd72d2e
children eb4910c5de12
files sorting.xml test-data/sorting_result3.fasta test-data/sorting_result4.fasta test-data/sorting_result5.fasta
diffstat 4 files changed, 168 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/sorting.xml	Sun Jun 28 22:49:34 2015 -0400
+++ b/sorting.xml	Wed Aug 26 08:11:49 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="vsearch_sorting" name="VSearch sorting" version="@VERSION@.0">
+<tool id="vsearch_sorting" name="VSearch sorting" version="@VERSION@.1">
     <description></description>
     <macros>
         <import>vsearch_macros.xml</import>
@@ -22,9 +22,10 @@
             #end if
         #end if
         --output $outfile
-        #if $sizeout:
-            --sizeout $sizeout
+        #if $relabel:
+            --relabel "$relabel"
         #end if
+        $sizeout
         #if $topn:
             --topn $topn
         #end if
@@ -49,6 +50,8 @@
           </when>
         </conditional>
         <expand macro="topn" />
+        <param name="relabel" type="text" value="" 
+               label="Relabel with this prefix string after sorting" help="(--relabel)"/>
         <param name="sizeout" type="boolean" truevalue="--sizeout" falsevalue="" checked="False" 
             label="Add abundance annotation to output" help="(--sizeout)"/>
     </inputs>
@@ -66,6 +69,24 @@
             <param name="infile" value="db.fasta" ftype="fasta" />
             <output name="outfile" file="sorting_result2.fasta" ftype="fasta" />
         </test>
+        <test>
+            <param name="sorting_mode_select" value="sortbylength"/>
+            <param name="infile" value="db.fasta" ftype="fasta" />
+            <param name="relabel" value="TEST" />
+            <output name="outfile" file="sorting_result3.fasta" ftype="fasta" />
+        </test>
+        <test>
+            <param name="sorting_mode_select" value="sortbylength"/>
+            <param name="infile" value="db.fasta" ftype="fasta" />
+            <param name="sizeout" value="--sizeout" />
+            <output name="outfile" file="sorting_result4.fasta" ftype="fasta" />
+        </test>
+        <test>
+            <param name="sorting_mode_select" value="sortbylength"/>
+            <param name="infile" value="db.fasta" ftype="fasta" />
+            <param name="relabel" value="With spaces" />
+            <output name="outfile" file="sorting_result5.fasta" ftype="fasta" />
+        </test>
     </tests>
     <help>
 <![CDATA[
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sorting_result3.fasta	Wed Aug 26 08:11:49 2015 -0400
@@ -0,0 +1,48 @@
+>TEST1
+MDVTVVVSTADHANVKRRRRRSHVRNRRARGYKSSRARSARMHGVDVDWDVVRSSVTSVSYSDDTDWAGNWAGS
+>TEST2
+MSRVVTAVASARATGDSGMGYVHATKTADTTTMRVAARDWVTGRSSKDYWSTTGKSGWDSTAVTTASAK
+>TEST3
+MRGTRRGSGGWSGARYAGSVAASDRSDTRATTSAYRHTHAASGARTRAHARHARHRVTVHVVAGVCARV
+>TEST4
+MGVYKCYNKKKVGVAVKRYVTKKSYKTANSNADSYNCRKCCKAKGCCDRYWKTVKNDKCKKGVVVYY
+>TEST5
+MTVSNTVDYTVSGDRSKKDCNRTCGWRDVRCRTKGTGNSTVTVTKARTVDAVKKMKRTTNSDA
+>TEST6
+MVSTRKKNSVYTGRKYGSYHKDDKKYADNKNRKRYVYSVDDAKAKATAKSVD
+>TEST7
+MTGAGTSGKKNTTTHTKCRRCGKSYHTKKKVCSSCGGKSAKRRDYWSKAG
+>TEST8
+MTGSGTSGKKNKTVHVKCRRCGASYHKTKKVCASCGGKSAKRRDYAWKAG
+>TEST9
+MSANNDTGHAAKRTDSRHTCRRCDRGVGKYDNCRCRVARDMGKYS
+>TEST10
+MSANNDTGHAAKRTDSRHTCRRCDRGVGKYDNCRCRVARDMGKYS
+>TEST11
+MSANNDTGHAAKRTDSRHTCRRCDRGVGKYDNCRCRVARDMGKYS
+>TEST12
+MSANNDTGHAAKRTDSRHTCRRCDRGVGKYDNCRCRVARDMGKYS
+>TEST13
+MSSTDTGHATKRTGDCRCGRKGVGKYDWCRCRARGMGRKYK
+>TEST14
+MSTVTGKSRDGYSTTDANNVARHVYSGSHGKRSDVSA
+>TEST15
+MSTYTVRGSARDGKVDANNVARVYSDGSHNKRTTVAA
+>TEST16
+MSTVTGKSRDGYATTDANNVARHVSGSHGKRTDVS
+>TEST17
+MTNAGRSKACDCKRKVGCSRYK
+>TEST18
+MTNAGRSKACDCKRKVGCSRYK
+>TEST19
+MATDSWAAVDAAASRTSYSTS
+>TEST20
+MRVRVDRVGVVGGGTKKRGV
+>TEST21
+KRGAHGKMNGSVKTTMGSGR
+>TEST22
+MSSNATSTGNMNSNHRDSST
+>TEST23
+MAHSDNRDTADYGGAHAA
+>TEST24
+MMDGSDMDDWRDD
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sorting_result4.fasta	Wed Aug 26 08:11:49 2015 -0400
@@ -0,0 +1,48 @@
+>sp|Q66125|2B_CMVQ Suppressor of silencing 2b OS=Cucumber mosaic virus (strain Q) GN=ORF2b PE=1 SV=1
+MDVTVVVSTADHANVKRRRRRSHVRNRRARGYKSSRARSARMHGVDVDWDVVRSSVTSVSYSDDTDWAGNWAGS
+>sp|P0DMP9|APOC3_PANTA Apolipoprotein C-III OS=Panthera tigris altaica GN=APOC3 PE=3 SV=1
+MSRVVTAVASARATGDSGMGYVHATKTADTTTMRVAARDWVTGRSSKDYWSTTGKSGWDSTAVTTASAK
+>sp|Q89681|DR4_HHV6U Uncharacterized protein DR4 OS=Human herpesvirus 6A (strain Uganda-1102) GN=DR4L PE=4 SV=1
+MRGTRRGSGGWSGARYAGSVAASDRSDTRATTSAYRHTHAASGARTRAHARHARHRVTVHVVAGVCARV
+>sp|Q91G65|032R_IIV6 Uncharacterized protein 032R OS=Invertebrate iridescent virus 6 GN=IIV6-032R PE=4 SV=1
+MGVYKCYNKKKVGVAVKRYVTKKSYKTANSNADSYNCRKCCKAKGCCDRYWKTVKNDKCKKGVVVYY
+>sp|B3MQ24|ENY2_DROAN Enhancer of yellow 2 transcription factor OS=Drosophila ananassae GN=e(y)2 PE=3 SV=1
+MTVSNTVDYTVSGDRSKKDCNRTCGWRDVRCRTKGTGNSTVTVTKARTVDAVKKMKRTTNSDA
+>sp|P20194|A100_SSV1 Uncharacterized protein A-100 OS=Sulfolobus spindle-shape virus 1 GN=a100 PE=1 SV=1
+MVSTRKKNSVYTGRKYGSYHKDDKKYADNKNRKRYVYSVDDAKAKATAKSVD
+>tr|M0KT65|M0KT65_9EURY 50S ribosomal protein L37e OS=Haloarcula amylolytica JCM 13557 GN=rpl37e PE=3 SV=1
+MTGAGTSGKKNTTTHTKCRRCGKSYHTKKKVCSSCGGKSAKRRDYWSKAG
+>tr|M0MK44|M0MK44_9EURY 50S ribosomal protein L37e OS=Halococcus saccharolyticus DSM 5350 GN=rpl37e PE=3 SV=1
+MTGSGTSGKKNKTVHVKCRRCGASYHKTKKVCASCGGKSAKRRDYAWKAG
+>tr|M0D8K9|M0D8K9_9EURY 30S ribosomal protein S14 type Z OS=Halorubrum terrestre JCM 10247 GN=rps14P PE=3 SV=1
+MSANNDTGHAAKRTDSRHTCRRCDRGVGKYDNCRCRVARDMGKYS
+>tr|M0F5C2|M0F5C2_9EURY 30S ribosomal protein S14 type Z OS=Halorubrum hochstenium ATCC 700873 GN=rps14P PE=3 SV=1
+MSANNDTGHAAKRTDSRHTCRRCDRGVGKYDNCRCRVARDMGKYS
+>tr|M0NIQ6|M0NIQ6_9EURY 30S ribosomal protein S14 type Z OS=Halorubrum lipolyticum DSM 21995 GN=rps14P PE=3 SV=1
+MSANNDTGHAAKRTDSRHTCRRCDRGVGKYDNCRCRVARDMGKYS
+>tr|M0PIT7|M0PIT7_9EURY 30S ribosomal protein S14 type Z OS=Halorubrum arcis JCM 13916 GN=rps14P PE=3 SV=1
+MSANNDTGHAAKRTDSRHTCRRCDRGVGKYDNCRCRVARDMGKYS
+>tr|M0MEH5|M0MEH5_9EURY 30S ribosomal protein S14 type Z OS=Halococcus saccharolyticus DSM 5350 GN=rps14P PE=3 SV=1
+MSSTDTGHATKRTGDCRCGRKGVGKYDWCRCRARGMGRKYK
+>tr|L9WHT8|L9WHT8_9EURY 50S ribosomal protein L18Ae OS=Natronorubrum bangense JCM 10635 GN=rplX PE=3 SV=1
+MSTVTGKSRDGYSTTDANNVARHVYSGSHGKRSDVSA
+>tr|M0KH83|M0KH83_9EURY 50S ribosomal protein L18Ae OS=Haloarcula amylolytica JCM 13557 GN=rplX PE=3 SV=1
+MSTYTVRGSARDGKVDANNVARVYSDGSHNKRTTVAA
+>tr|L9WBT3|L9WBT3_9EURY 50S ribosomal protein L18Ae OS=Natronorubrum sulfidifaciens JCM 14089 GN=rplX PE=3 SV=1
+MSTVTGKSRDGYATTDANNVARHVSGSHGKRTDVS
+>tr|W9PMP6|W9PMP6_FUSOX Uncharacterized protein OS=Fusarium oxysporum f. sp. pisi HDV247 GN=FOVG_07074 PE=4 SV=1
+MTNAGRSKACDCKRKVGCSRYK
+>tr|X0LYM3|X0LYM3_FUSOX Uncharacterized protein OS=Fusarium oxysporum f. sp. vasinfectum 25433 GN=FOTG_17987 PE=4 SV=1
+MTNAGRSKACDCKRKVGCSRYK
+>tr|H3BPV3|H3BPV3_HUMAN ATP-dependent RNA helicase DDX19B OS=Homo sapiens GN=DDX19B PE=4 SV=1
+MATDSWAAVDAAASRTSYSTS
+>tr|H0ACG9|H0ACG9_HALSG Uncharacterized protein OS=Haloredivivus sp. (strain G17) GN=HRED_08116 PE=4 SV=1
+MRVRVDRVGVVGGGTKKRGV
+>tr|N6VV02|N6VV02_9EURY Uncharacterized protein (Fragment) OS=Thermoplasmatales archaeon SCGC AB-539-C06 GN=MBGDC06_00209 PE=4 SV=1
+KRGAHGKMNGSVKTTMGSGR
+>tr|Q53RS6|Q53RS6_HUMAN Putative uncharacterized protein ALS2CR3 (Fragment) OS=Homo sapiens GN=ALS2CR3 PE=4 SV=1
+MSSNATSTGNMNSNHRDSST
+>tr|V9H0X7|V9H0X7_NEUCS Neurospora crassa DNA for RNA polymerase I second-largest subunit OS=Neurospora crassa PE=4 SV=1
+MAHSDNRDTADYGGAHAA
+>tr|Q9BZF8|Q9BZF8_HUMAN NF-E2-related factor 2 (Fragment) OS=Homo sapiens PE=2 SV=1
+MMDGSDMDDWRDD
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sorting_result5.fasta	Wed Aug 26 08:11:49 2015 -0400
@@ -0,0 +1,48 @@
+>With spaces1
+MDVTVVVSTADHANVKRRRRRSHVRNRRARGYKSSRARSARMHGVDVDWDVVRSSVTSVSYSDDTDWAGNWAGS
+>With spaces2
+MSRVVTAVASARATGDSGMGYVHATKTADTTTMRVAARDWVTGRSSKDYWSTTGKSGWDSTAVTTASAK
+>With spaces3
+MRGTRRGSGGWSGARYAGSVAASDRSDTRATTSAYRHTHAASGARTRAHARHARHRVTVHVVAGVCARV
+>With spaces4
+MGVYKCYNKKKVGVAVKRYVTKKSYKTANSNADSYNCRKCCKAKGCCDRYWKTVKNDKCKKGVVVYY
+>With spaces5
+MTVSNTVDYTVSGDRSKKDCNRTCGWRDVRCRTKGTGNSTVTVTKARTVDAVKKMKRTTNSDA
+>With spaces6
+MVSTRKKNSVYTGRKYGSYHKDDKKYADNKNRKRYVYSVDDAKAKATAKSVD
+>With spaces7
+MTGAGTSGKKNTTTHTKCRRCGKSYHTKKKVCSSCGGKSAKRRDYWSKAG
+>With spaces8
+MTGSGTSGKKNKTVHVKCRRCGASYHKTKKVCASCGGKSAKRRDYAWKAG
+>With spaces9
+MSANNDTGHAAKRTDSRHTCRRCDRGVGKYDNCRCRVARDMGKYS
+>With spaces10
+MSANNDTGHAAKRTDSRHTCRRCDRGVGKYDNCRCRVARDMGKYS
+>With spaces11
+MSANNDTGHAAKRTDSRHTCRRCDRGVGKYDNCRCRVARDMGKYS
+>With spaces12
+MSANNDTGHAAKRTDSRHTCRRCDRGVGKYDNCRCRVARDMGKYS
+>With spaces13
+MSSTDTGHATKRTGDCRCGRKGVGKYDWCRCRARGMGRKYK
+>With spaces14
+MSTVTGKSRDGYSTTDANNVARHVYSGSHGKRSDVSA
+>With spaces15
+MSTYTVRGSARDGKVDANNVARVYSDGSHNKRTTVAA
+>With spaces16
+MSTVTGKSRDGYATTDANNVARHVSGSHGKRTDVS
+>With spaces17
+MTNAGRSKACDCKRKVGCSRYK
+>With spaces18
+MTNAGRSKACDCKRKVGCSRYK
+>With spaces19
+MATDSWAAVDAAASRTSYSTS
+>With spaces20
+MRVRVDRVGVVGGGTKKRGV
+>With spaces21
+KRGAHGKMNGSVKTTMGSGR
+>With spaces22
+MSSNATSTGNMNSNHRDSST
+>With spaces23
+MAHSDNRDTADYGGAHAA
+>With spaces24
+MMDGSDMDDWRDD