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comparison chimera.ccode.xml @ 2:ad1b47de42a3 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 22:06:21 -0400
parents 3eca08ae427b
children 79255ca0b19a
comparison
equal deleted inserted replaced
1:502024707de4 2:ad1b47de42a3
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 "$fasta" fasta.dat && 13 ln -s '$fasta' fasta.dat &&
14 ln -s "$alignment.template" alignment.template.dat && 14 ln -s '$alignment.reference' alignment.template.dat &&
15 #if $mask.source2 == "history": 15 #if $mask_cond.source2 == "history":
16 ln -s "$mask.input" mask.input.dat && 16 ln -s '$mask_cond.input' mask_cond.mask.dat &&
17 #end if 17 #end if
18 18
19 echo 'chimera.ccode( 19 echo 'chimera.ccode(
20 fasta=fasta.dat, 20 fasta=fasta.dat,
21 reference=alignment.template.dat, 21 reference=alignment.template.dat,
22 filter=$filter, 22 filter=$filter,
23 #if $mask.source2 == "default": 23 #if $mask_cond.source2 == "default":
24 mask=default, 24 mask=default,
25 #elif $mask.source2 == "history": 25 #elif $mask_cond.source2 == "history":
26 mask=mask.input.dat, 26 mask=mask_cond.mask.dat,
27 #end if 27 #end if
28 #if int($window) > 0: 28 #if int($window) > 0:
29 window=$window, 29 window=$window,
30 #end if 30 #end if
31 #if int($numwanted) > 0: 31 #if int($numwanted) > 0:
32 numwanted=$numwanted, 32 numwanted=$numwanted,
33 #end if 33 #end if
34 processors='\${GALAXY_SLOTS:-8}' 34 processors='\${GALAXY_SLOTS:-8}'
35 )' 35 )'
36 | sed 's/ //g' ## mothur trips over whitespace 36 | sed 's/ //g' ## mothur trips over whitespace
37 | mothur 37 | mothur
38 | tee mothur.out.log 38 | tee mothur.out.log
39 ]]></command> 39 ]]></command>
40 <inputs> 40 <inputs>
41 <param name="fasta" type="data" format="mothur.align" label="fasta - Candiate Aligned Sequences"/> 41 <param argument="fasta" type="data" format="mothur.align" label="fasta - Candiate Aligned Sequences"/>
42 <conditional name="alignment"> 42 <conditional name="alignment">
43 <param name="source" type="select" label="Select Reference Template from" help=""> 43 <param name="source" type="select" label="Select Reference Template from">
44 <option value="hist">History</option> 44 <option value="hist">History</option>
45 <option value="ref">Cached Reference</option> 45 <option value="ref">Cached Reference</option>
46 </param> 46 </param>
47 <when value="ref"> 47 <when value="ref">
48 <param name="template" type="select" label="reference - Select an alignment database" help=""> 48 <param argument="reference" type="select" label="reference - Select an alignment database">
49 <options from_data_table="mothur_aligndb"> 49 <options from_data_table="mothur_aligndb"/>
50 </options>
51 </param> 50 </param>
52 </when> 51 </when>
53 <when value="hist"> 52 <when value="hist">
54 <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/> 53 <param argument="reference" type="data" format="fasta" label="reference - Reference to align with"/>
55 </when> 54 </when>
56 </conditional> 55 </conditional>
57 <param name="filter" type="boolean" falsevalue="False" truevalue="True" checked="false" label="filter - Apply a 50% soft vertical filter"/> 56 <param argument="filter" type="boolean" falsevalue="False" truevalue="True" checked="false" label="filter - Apply a 50% soft vertical filter"/>
58 <conditional name="mask"> 57 <conditional name="mask_cond">
59 <param name="source2" type="select" label="Mask option"> 58 <param name="source2" type="select" label="Mask option">
60 <option value="">None</option> 59 <option value="">None</option>
61 <option value="default">default ecoli mask</option> 60 <option value="default">default ecoli mask</option>
62 <option value="history">From Your History</option> 61 <option value="history">From Your History</option>
63 </param> 62 </param>
64 <when value="history"> 63 <when value="history">
65 <param name="input" type="data" format="mothur.filter" label="Mask for the reference file" help=""/> 64 <param argument="mask" type="data" format="mothur.filter" label="Mask for the reference file"/>
66 </when> 65 </when>
67 <when value=""/> 66 <when value=""/>
68 <when value="default"/> 67 <when value="default"/>
69 </conditional> 68 </conditional>
70 <param name="window" type="integer" value="0" label="window - Length of sequence you want in each window analyzed (default if &lt; 1)" help="Recommended window size is between 5 and 20% of your trimmed sequence length. Default is 10% of the sequence length."/> 69 <param name="window" type="integer" value="0" label="window - Length of sequence you want in each window analyzed"
71 <param name="numwanted" type="integer" value="20" label="numwanted - Number of sequences compared with each query (uses default if set to 0)"/> 70 help="Recommended window size is between 5 and 20% of your trimmed sequence length. Default is 10% of the sequence length. Default is used if &lt; 1"/>
71 <param name="numwanted" type="integer" value="20" label="numwanted - Number of sequences compared with each query"
72 help="uses default if set to 0"/>
73 <expand macro="param-savelog"/>
72 </inputs> 74 </inputs>
73 <outputs> 75 <outputs>
74 <expand macro="logfile-output"/> 76 <expand macro="logfile-output"/>
75 <data name="out_file" format="txt" from_work_dir="fasta.*ccode.chimeras" label="${tool.name} on ${on_string}: ccode.chimeras"/> 77 <data name="ccode.chimeras" format="txt" from_work_dir="fasta.*ccode.chimeras" label="${tool.name} on ${on_string}: ccode.chimeras"/>
76 <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*ccode.accnos" label="${tool.name} on ${on_string}: ccode.accnos"/> 78 <data name="ccode.accnos" format="mothur.accnos" from_work_dir="fasta.*ccode.accnos" label="${tool.name} on ${on_string}: ccode.accnos"/>
77 <data name="mapinfo" format="tabular" from_work_dir="*.mapinfo" label="${tool.name} on ${on_string}: mapinfo"/> 79 <data name="mapinfo" format="tabular" from_work_dir="*.mapinfo" label="${tool.name} on ${on_string}: mapinfo"/>
78 </outputs> 80 </outputs>
79 <tests> 81 <tests>
80 <test> 82 <test>
81 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/> 83 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
82 <param name="source" value="hist"/> 84 <param name="source" value="hist"/>
83 <param name="template" value="HMP_MOCK.v35.align"/> 85 <param name="reference" value="HMP_MOCK.v35.align"/>
84 <output name="out_file" ftype="txt"> 86 <output name="ccode.chimeras" ftype="txt">
85 <assert_contents> 87 <assert_contents>
86 <has_line_matching expression="^Window\tAvgQ\t\(sdQ\)\tAvgR\t\(sdR\)\tRatio\tAnova$"/> 88 <has_line_matching expression="^Window\tAvgQ\t\(sdQ\)\tAvgR\t\(sdR\)\tRatio\tAnova$"/>
87 </assert_contents> 89 </assert_contents>
88 </output> 90 </output>
89 <output name="out_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ccode.accnos" ftype="mothur.accnos"/> 91 <output name="ccode.accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ccode.accnos" ftype="mothur.accnos"/>
90 <output name="mapinfo" md5="ef3353b1467fe95a24153513917e6444" ftype="tabular"/> 92 <output name="mapinfo" md5="ef3353b1467fe95a24153513917e6444" ftype="tabular"/>
93 <param name="savelog" value="true"/>
91 <expand macro="logfile-test"/> 94 <expand macro="logfile-test"/>
92 </test> 95 </test>
93 <test> <!-- test with default ecoli mask --> 96 <test> <!-- test with default ecoli mask -->
94 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/> 97 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
95 <param name="source" value="hist"/> 98 <param name="source" value="hist"/>
96 <param name="template" value="HMP_MOCK.v35.align"/> 99 <param name="reference" value="HMP_MOCK.v35.align"/>
97 <param name="source2" value="default"/> 100 <param name="source2" value="default"/>
98 <param name="window" value="100"/> 101 <param name="window" value="100"/>
99 <output name="out_file" ftype="txt"> 102 <output name="ccode.chimeras" ftype="txt">
100 <assert_contents> 103 <assert_contents>
101 <has_line_matching expression="^Window\tAvgQ\t\(sdQ\)\tAvgR\t\(sdR\)\tRatio\tAnova$"/> 104 <has_line_matching expression="^Window\tAvgQ\t\(sdQ\)\tAvgR\t\(sdR\)\tRatio\tAnova$"/>
102 </assert_contents> 105 </assert_contents>
103 </output> 106 </output>
104 <output name="out_accnos" md5="47ddf86ec36aafd495aa902b3e06ffca" ftype="mothur.accnos"/> 107 <output name="ccode.accnos" md5="47ddf86ec36aafd495aa902b3e06ffca" ftype="mothur.accnos"/>
105 <output name="mapinfo" md5="25221b1e109d9c0a939efb319e7a9896" ftype="tabular"/> 108 <output name="mapinfo" md5="25221b1e109d9c0a939efb319e7a9896" ftype="tabular"/>
109 <param name="savelog" value="true"/>
106 <expand macro="logfile-test"/> 110 <expand macro="logfile-test"/>
107 </test> 111 </test>
108 </tests> 112 </tests>
109 <help> 113 <help><![CDATA[
110 <![CDATA[
111 114
112 @MOTHUR_OVERVIEW@ 115 @MOTHUR_OVERVIEW@
113 116
114 **Command Documentation** 117 **Command Documentation**
115 118
121 124
122 .. _Ccode: http://www.microextreme.net/downloads.html 125 .. _Ccode: http://www.microextreme.net/downloads.html
123 .. _paper: http://bioinformatics.oxfordjournals.org/content/21/3/333.full.pdf 126 .. _paper: http://bioinformatics.oxfordjournals.org/content/21/3/333.full.pdf
124 .. _chimera.ccode: https://www.mothur.org/wiki/Chimera.ccode 127 .. _chimera.ccode: https://www.mothur.org/wiki/Chimera.ccode
125 128
126 ]]> 129 ]]></help>
127 </help>
128 <expand macro="citations"/> 130 <expand macro="citations"/>
129 </tool> 131 </tool>