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comparison sffinfo.xml @ 0:b2c31e79e969 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:40:20 -0400
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children 32a19ce534d1
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-1:000000000000 0:b2c31e79e969
1 <tool profile="16.07" id="mothur_sffinfo" name="Sffinfo" version="@WRAPPER_VERSION@.0">
2 <description>Summarize the quality of sequences</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$sff" sff.dat &&
11 ln -s "$accnos" accnos.dat &&
12 #if $oligo.add == "yes":
13 ln -s "$oligo.oligos" oligo.oligos.dat &&
14 #end if
15
16 echo 'sffinfo(
17 sff=sff.dat,
18 fasta=$fasta,
19 qfile=$qfile,
20 $sfftxt
21 flow=$flow,
22 trim=$trim
23 #if $accnos:
24 ,accnos=accnos.dat
25 #end if
26 #if $oligo.add == "yes":
27 ,oligos=oligo.oligos.dat
28 ,bdiffs=$oligo.bdiffs
29 ,pdiffs=$oligo.pdiffs
30 ,tdiffs=$oligo.tdiffs
31 ,ldiffs=$oligo.ldiffs
32 ,sdiffs=$oligo.sdiffs
33 #end if
34 )'
35 | sed 's/ //g' ## mothur trips over whitespace
36 | mothur
37 ]]></command>
38 <inputs>
39 <param name="sff" type="data" format="sff" label="sff - Sff data"/>
40 <conditional name="oligo">
41 <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.">
42 <option value="no" selected="true">no</option>
43 <option value="yes">yes</option>
44 </param>
45 <when value="no"/>
46 <when value="yes">
47 <param name="oligos" type="data" format="mothur.oligos" label="oligos - barcodes and primers"/>
48 <param name="bdiffs" type="integer" value="0" min="0" label="bdiffs - number of differences to allow in the barcode (default 0)"/>
49 <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (default 0)"/>
50 <param name="tdiffs" type="integer" value="0" min="0" label="tdiffs - total number of differences to allow in primer and barcode (default 0)"/>
51 <param name="ldiffs" type="integer" value="0" min="0" label="ldiffs - total number of differences to allow in linker sequence (default 0)"/>
52 <param name="sdiffs" type="integer" value="0" min="0" label="sdiffs - total number of differences to allow in spacer sequence (default 0)"/>
53 </when>
54 </conditional>
55 <param name="fasta" type="boolean" truevalue="true" falsevalue="false" checked="true" label="fasta - Add fasta to your history"/>
56 <param name="qfile" type="boolean" truevalue="true" falsevalue="false" checked="true" label="qfile - Add qfile to your history"/>
57 <param name="sfftxt" type="boolean" truevalue="sfftxt=true," falsevalue="" checked="false" label="sfftxt - Add sfftxt to your history"/>
58 <param name="flow" type="boolean" truevalue="true" falsevalue="false" checked="true" label="flow - Add flow to your history"/>
59 <param name="trim" type="boolean" truevalue="true" falsevalue="false" checked="true" label="trim - Trim sequences and quality scores"/>
60 <param name="accnos" type="data" format="mothur.accnos" optional="true" label="accnos - Limit output to named Accessions"/>
61 </inputs>
62 <outputs>
63 <expand macro="logfile-output"/>
64 <data name="out_fasta" format="fasta" from_work_dir="sff*.fasta" label="${tool.name} on ${on_string}: fasta">
65 <filter>fasta</filter>
66 </data>
67 <data name="out_qfile" format="qual454" from_work_dir="sff*.qual" label="${tool.name} on ${on_string}: qual">
68 <filter>qfile</filter>
69 </data>
70 <data name="out_sfftxt" format="txt" from_work_dir="sff*.sff.txt" label="${tool.name} on ${on_string}: sff.txt">
71 <filter>sfftxt</filter>
72 </data>
73 <data name="out_flow" format="mothur.sff.flow" from_work_dir="sff*.flow" label="${tool.name} on ${on_string}: flowgram">
74 <filter>flow</filter>
75 </data>
76 <data name="out_scrap" format="sff" from_work_dir="sff*.scrap.sff" label="${tool.name} on ${on_string}: scrap.sff">
77 <filter>oligo['add'] == 'yes'</filter>
78 </data>
79 </outputs>
80 <tests>
81 <test><!-- test without oligos -->
82 <param name="sff" value="Fasting_Example1.sff"/>
83 <param name="sfftxt" value="true"/>
84 <output name="out_fasta" md5="fbe6f4d51959d4723a8417636476d0e0" ftype="fasta"/>
85 <output name="out_qfile" md5="ffcc4831369139055e1b8e9add9a59c0" ftype="qual454"/>
86 <output name="out_sfftxt" md5="fdc80c8e476016632d317cfd7893713c" ftype="txt"/>
87 <output name="out_flow" md5="34b17477f98ab19c1ff755a61848d968" ftype="mothur.sff.flow"/>
88 <expand macro="logfile-test"/>
89 </test>
90 <test><!-- test with oligos file -->
91 <param name="sff" value="Fasting_Example1.sff"/>
92 <param name="add" value="yes"/>
93 <param name="oligos" value="GQY1XT001.oligos"/>
94 <output name="out_fasta" md5="212fa15e1ed077cecb65ee87f17ef2e1" ftype="fasta"/>
95 <output name="out_qfile" md5="ffcc4831369139055e1b8e9add9a59c0" ftype="qual454"/>
96 <output name="out_flow" md5="34b17477f98ab19c1ff755a61848d968" ftype="mothur.sff.flow"/>
97 <output name="out_scrap" md5="f03c422fe364815e7214ad31ad135aca" ftype="sff"/>
98 <expand macro="logfile-test"/>
99 </test>
100 </tests>
101 <help>
102 <![CDATA[
103
104 @MOTHUR_OVERVIEW@
105
106 **Command Documenation**
107
108 The sffinfo_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file.
109
110
111 .. _sffinfo: http://www.mothur.org/wiki/Sffinfo
112 ]]>
113 </help>
114 <expand macro="citations"/>
115 </tool>