Mercurial > repos > iuc > mothur_sffinfo

comparison sffinfo.xml @ 2:13d1e5e44a91 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:19:08 -0400
parents 5ada2d00e874
children 51d7c2486a68
comparison
equal deleted inserted replaced
1:5d52096c0a9c 2:13d1e5e44a91
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$sff" sff.dat && 13 ln -s '$sff' sff.dat &&
14 ln -s "$accnos" accnos.dat && 14 ln -s '$accnos' accnos.dat &&
15 #if $oligo.add == "yes": 15 #if $oligo.add == "yes":
16 ln -s "$oligo.oligos" oligo.oligos.dat && 16 ln -s '$oligo.oligos' oligo.oligos.dat &&
17 #end if 17 #end if
18 18
19 echo 'sffinfo( 19 echo 'sffinfo(
20 sff=sff.dat, 20 sff=sff.dat,
21 fasta=$fasta, 21 fasta=$fasta,
22 qfile=$qfile, 22 qfile=$qfile,
23 $sfftxt 23 $sfftxt
24 flow=$flow, 24 flow=$flow,
25 trim=$trim 25 trim=$trim
26 #if $accnos: 26 #if $accnos:
27 ,accnos=accnos.dat 27 ,accnos=accnos.dat
28 #end if 28 #end if
29 #if $oligo.add == "yes": 29 #if $oligo.add == "yes":
30 ,oligos=oligo.oligos.dat 30 ,oligos=oligo.oligos.dat
31 ,bdiffs=$oligo.bdiffs 31 ,bdiffs=$oligo.bdiffs
32 ,pdiffs=$oligo.pdiffs 32 ,pdiffs=$oligo.pdiffs
33 ,tdiffs=$oligo.tdiffs 33 ,tdiffs=$oligo.tdiffs
34 ,ldiffs=$oligo.ldiffs 34 ,ldiffs=$oligo.ldiffs
35 ,sdiffs=$oligo.sdiffs 35 ,sdiffs=$oligo.sdiffs
36 #end if 36 #end if
37 )' 37 )'
38 | sed 's/ //g' ## mothur trips over whitespace 38 | sed 's/ //g' ## mothur trips over whitespace
39 | mothur 39 | mothur
40 | tee mothur.out.log 40 | tee mothur.out.log
41 ]]></command> 41 ]]></command>
42 <inputs> 42 <inputs>
43 <param name="sff" type="data" format="sff" label="sff - Sff data"/> 43 <param name="sff" type="data" format="sff" label="sff - Sff data"/>
44 <conditional name="oligo"> 44 <conditional name="oligo">
45 <param name="add" type="select" label="Trim with an oligos file?" help="a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier. Each line of the oligos file can start with the key words &quot;forward&quot;, &quot;reverse&quot;, and &quot;barcode&quot; or it can start with a &quot;#&quot; to tell mothur to ignore that line of the oligos file."> 45 <param name="add" type="select" label="Trim with an oligos file?" help="a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier. Each line of the oligos file can start with the key words &quot;forward&quot;, &quot;reverse&quot;, and &quot;barcode&quot; or it can start with a &quot;#&quot; to tell mothur to ignore that line of the oligos file.">
60 <param name="qfile" type="boolean" truevalue="true" falsevalue="false" checked="true" label="qfile - Add qfile to your history"/> 60 <param name="qfile" type="boolean" truevalue="true" falsevalue="false" checked="true" label="qfile - Add qfile to your history"/>
61 <param name="sfftxt" type="boolean" truevalue="sfftxt=true," falsevalue="" checked="false" label="sfftxt - Add sfftxt to your history"/> 61 <param name="sfftxt" type="boolean" truevalue="sfftxt=true," falsevalue="" checked="false" label="sfftxt - Add sfftxt to your history"/>
62 <param name="flow" type="boolean" truevalue="true" falsevalue="false" checked="true" label="flow - Add flow to your history"/> 62 <param name="flow" type="boolean" truevalue="true" falsevalue="false" checked="true" label="flow - Add flow to your history"/>
63 <param name="trim" type="boolean" truevalue="true" falsevalue="false" checked="true" label="trim - Trim sequences and quality scores"/> 63 <param name="trim" type="boolean" truevalue="true" falsevalue="false" checked="true" label="trim - Trim sequences and quality scores"/>
64 <param name="accnos" type="data" format="mothur.accnos" optional="true" label="accnos - Limit output to named Accessions"/> 64 <param name="accnos" type="data" format="mothur.accnos" optional="true" label="accnos - Limit output to named Accessions"/>
65 <expand macro="param-savelog"/>
65 </inputs> 66 </inputs>
66 <outputs> 67 <outputs>
67 <expand macro="logfile-output"/> 68 <expand macro="logfile-output"/>
68 <data name="out_fasta" format="fasta" from_work_dir="sff*.fasta" label="${tool.name} on ${on_string}: fasta"> 69 <data name="out_fasta" format="fasta" from_work_dir="sff*.fasta" label="${tool.name} on ${on_string}: fasta">
69 <filter>fasta</filter> 70 <filter>fasta</filter>
87 <param name="sfftxt" value="true"/> 88 <param name="sfftxt" value="true"/>
88 <output name="out_fasta" md5="fbe6f4d51959d4723a8417636476d0e0" ftype="fasta"/> 89 <output name="out_fasta" md5="fbe6f4d51959d4723a8417636476d0e0" ftype="fasta"/>
89 <output name="out_qfile" md5="ffcc4831369139055e1b8e9add9a59c0" ftype="qual454"/> 90 <output name="out_qfile" md5="ffcc4831369139055e1b8e9add9a59c0" ftype="qual454"/>
90 <output name="out_sfftxt" md5="fdc80c8e476016632d317cfd7893713c" ftype="txt"/> 91 <output name="out_sfftxt" md5="fdc80c8e476016632d317cfd7893713c" ftype="txt"/>
91 <output name="out_flow" md5="34b17477f98ab19c1ff755a61848d968" ftype="mothur.sff.flow"/> 92 <output name="out_flow" md5="34b17477f98ab19c1ff755a61848d968" ftype="mothur.sff.flow"/>
93 <param name="savelog" value="true"/>
92 <expand macro="logfile-test"/> 94 <expand macro="logfile-test"/>
93 </test> 95 </test>
94 <test><!-- test with oligos file --> 96 <test><!-- test with oligos file -->
95 <param name="sff" value="Fasting_Example1.sff"/> 97 <param name="sff" value="Fasting_Example1.sff"/>
96 <param name="add" value="yes"/> 98 <param name="add" value="yes"/>
97 <param name="oligos" value="GQY1XT001.oligos"/> 99 <param name="oligos" value="GQY1XT001.oligos"/>
98 <output name="out_fasta" md5="212fa15e1ed077cecb65ee87f17ef2e1" ftype="fasta"/> 100 <output name="out_fasta" md5="212fa15e1ed077cecb65ee87f17ef2e1" ftype="fasta"/>
99 <output name="out_qfile" md5="ffcc4831369139055e1b8e9add9a59c0" ftype="qual454"/> 101 <output name="out_qfile" md5="ffcc4831369139055e1b8e9add9a59c0" ftype="qual454"/>
100 <output name="out_flow" md5="34b17477f98ab19c1ff755a61848d968" ftype="mothur.sff.flow"/> 102 <output name="out_flow" md5="34b17477f98ab19c1ff755a61848d968" ftype="mothur.sff.flow"/>
101 <output name="out_scrap" md5="f03c422fe364815e7214ad31ad135aca" ftype="sff"/> 103 <output name="out_scrap" file="Fasting_Example1.scrap.sff" ftype="sff" compare="sim_size"/>
104 <param name="savelog" value="true"/>
102 <expand macro="logfile-test"/> 105 <expand macro="logfile-test"/>
103 </test> 106 </test>
104 </tests> 107 </tests>
105 <help> 108 <help><![CDATA[
106 <![CDATA[
107 109
108 @MOTHUR_OVERVIEW@ 110 @MOTHUR_OVERVIEW@
109 111
110 **Command Documentation** 112 **Command Documentation**
111 113
112 The sffinfo_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file. 114 The sffinfo_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file.
113 115
114 116
115 .. _sffinfo: https://www.mothur.org/wiki/Sffinfo 117 .. _sffinfo: https://www.mothur.org/wiki/Sffinfo
116 ]]> 118
117 </help> 119 ]]></help>
118 <expand macro="citations"/> 120 <expand macro="citations"/>
119 </tool> 121 </tool>