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comparison screen.seqs.xml @ 1:d0190913cb6c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:17:26 -0400
parents 5a01375eadf0
children 7dabd4117ad1
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0:5a01375eadf0 1:d0190913cb6c
2 <description>Screen sequences</description> 2 <description>Screen sequences</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
9 ## create symlinks to input datasets 12 ## create symlinks to input datasets
10 ln -s "$fasta_in" fasta_in.dat && 13 ln -s "$fasta_in" fasta_in.dat &&
11 ln -s "$names_in" names_in.dat && 14 ln -s "$names_in" names_in.dat &&
12 ln -s "$groups_in" groups_in.dat && 15 ln -s "$groups_in" groups_in.dat &&
13 ln -s "$qfile_in" qfile_in.dat && 16 ln -s "$qfile_in" qfile_in.dat &&
17 ln -s "$summary" summary.dat && 20 ln -s "$summary" summary.dat &&
18 ln -s "$contigsreport" contigsreport.dat && 21 ln -s "$contigsreport" contigsreport.dat &&
19 22
20 echo 'screen.seqs( 23 echo 'screen.seqs(
21 fasta=fasta_in.dat 24 fasta=fasta_in.dat
22 #if $start > -1: 25 #if int($start) > -1:
23 ,start=$start 26 ,start=$start
24 #end if 27 #end if
25 #if $end > -1: 28 #if int($end) > -1:
26 ,end=$end 29 ,end=$end
27 #end if 30 #end if
28 #if $minlength > -1: 31 #if int($minlength) > -1:
29 ,minlength=$minlength 32 ,minlength=$minlength
30 #end if 33 #end if
31 #if $maxlength > -1: 34 #if int($maxlength) > -1:
32 ,maxlength=$maxlength 35 ,maxlength=$maxlength
33 #end if 36 #end if
34 #if $maxambig > -1: 37 #if int($maxambig) > -1:
35 ,maxambig=$maxambig 38 ,maxambig=$maxambig
36 #end if 39 #end if
37 #if $maxhomop > -1: 40 #if int($maxhomop) > -1:
38 ,maxhomop=$maxhomop 41 ,maxhomop=$maxhomop
39 #end if 42 #end if
40 #if $criteria > -1: 43 #if int($criteria) > -1:
41 ,criteria=$criteria 44 ,criteria=$criteria
42 #end if 45 #end if
43 #if $optimize: 46 #if $optimize:
44 ,optimize=$optimize 47 ,optimize=$optimize
45 #end if 48 #end if
69 #end if 72 #end if
70 ,processors='"\${GALAXY_SLOTS:-8}"' 73 ,processors='"\${GALAXY_SLOTS:-8}"'
71 )' 74 )'
72 | sed 's/ //g' ## mothur trips over whitespace 75 | sed 's/ //g' ## mothur trips over whitespace
73 | mothur 76 | mothur
77 | tee mothur.out.log
74 ]]></command> 78 ]]></command>
75 <inputs> 79 <inputs>
76 <param name="fasta_in" type="data" format="fasta,mothur.align" label="fasta - Fasta to screen"/> 80 <param name="fasta_in" type="data" format="fasta,mothur.align" label="fasta - Fasta to screen"/>
77 <param name="start" type="integer" value="-1" label="start - Remove sequences that start after position (ignored when negative)"/> 81 <param name="start" type="integer" value="-1" label="start - Remove sequences that start after position (ignored when negative)"/>
78 <param name="end" type="integer" value="-1" label="end - Remove sequences that end before position (ignored when negative)"/> 82 <param name="end" type="integer" value="-1" label="end - Remove sequences that end before position (ignored when negative)"/>
91 </param> 95 </param>
92 <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Sequence Quality file to screen"/> 96 <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Sequence Quality file to screen"/>
93 <param name="names_in" type="data" format="mothur.names" optional="true" label="name - Sequence Names to screen"/> 97 <param name="names_in" type="data" format="mothur.names" optional="true" label="name - Sequence Names to screen"/>
94 <param name="groups_in" type="data" format="mothur.groups" optional="true" label="group - Groups to screen"/> 98 <param name="groups_in" type="data" format="mothur.groups" optional="true" label="group - Groups to screen"/>
95 <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report to screen"/> 99 <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report to screen"/>
96 <param name="summary" type="data" format="mothur.summary" optional="true" label="summary - allows you to enter the summary file created by summary.seqs to save processing time when screening with parameters in the summary file"/> 100 <param name="summary" type="data" format="mothur.summary" optional="true" label="summary file - as created by summary.seqs" help="saves processing time when screening with parameters in the summary file"/>
97 <param name="contigsreport" type="data" format="contigs.report" optional="true" label="contigsreport - Contigs Report to screen with" help="this file is created by the make.contigs command. If you provide the contigs report file you can screen your sequences using the following parameters: minoverlap, ostart, oend and mismatches"/> 101 <param name="contigsreport" type="data" format="contigs.report" optional="true" label="contigsreport - Contigs Report to screen with" help="this file is created by the make.contigs command. If you provide the contigs report file you can screen your sequences using the following parameters: minoverlap, ostart, oend and mismatches"/>
98 <param name="taxonomy_in" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/> 102 <param name="taxonomy_in" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/>
99 <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> 103 <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
100 </inputs> 104 </inputs>
101 <outputs> 105 <outputs>
112 <filter>groups_in</filter> 116 <filter>groups_in</filter>
113 </data> 117 </data>
114 <data name="alignreport_out" format="mothur.align.report" from_work_dir="alignreport_in*.good.dat" label="${tool.name} on ${on_string}: align.report"> 118 <data name="alignreport_out" format="mothur.align.report" from_work_dir="alignreport_in*.good.dat" label="${tool.name} on ${on_string}: align.report">
115 <filter>alignreport_in</filter> 119 <filter>alignreport_in</filter>
116 </data> 120 </data>
117 <data name="count_out" format="count" from_work_dir="count_in*.good.dat" label="${tool.name} on ${on_string}: count"> 121 <data name="count_out" format="mothur.count_table" from_work_dir="count_in*.good.dat" label="${tool.name} on ${on_string}: count">
118 <filter>count_in</filter> 122 <filter>count_in</filter>
119 </data> 123 </data>
120 </outputs> 124 </outputs>
121 <tests> 125 <tests>
122 <test> 126 <test>
123 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/> 127 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
124 <param name="maxambig" value="0"/> 128 <param name="maxambig" value="0"/>
125 <param name="maxlength" value="275"/> 129 <param name="maxlength" value="275"/>
126 <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta"/> 130 <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta" ftype="fasta"/>
127 <output name="bad_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/> 131 <output name="bad_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos" ftype="mothur.accnos"/>
128 <expand macro="logfile-test"/> 132 <expand macro="logfile-test"/>
129 </test> 133 </test>
130 <test> 134 <test>
131 <param name="fasta_in" value="amazon.fasta"/> 135 <param name="fasta_in" value="amazon.fasta" ftype="mothur.align"/>
132 <param name="count_in" value="amazon.count_table"/> 136 <param name="count_in" value="amazon.count_table"/>
133 <param name="maxambig" value="0"/> 137 <param name="maxambig" value="0"/>
134 <param name="maxlength" value="275"/> 138 <param name="maxlength" value="275"/>
135 <output name="fasta_out" md5="d41d8cd98f00b204e9800998ecf8427e"/> 139 <output name="fasta_out" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/>
136 <output name="count_out" md5="5f4a08bbf3ec12f954edbcc6b2a2feee"/> 140 <output name="count_out" md5="5f4a08bbf3ec12f954edbcc6b2a2feee" ftype="mothur.count_table"/>
137 <output name="bad_accnos" md5="66acde5349e34fc97be22032ce68eea5"/> 141 <output name="bad_accnos" md5="66acde5349e34fc97be22032ce68eea5" ftype="mothur.accnos"/>
138 <expand macro="logfile-test"/> 142 <expand macro="logfile-test"/>
139 </test> 143 </test>
140 </tests> 144 </tests>
141 <help> 145 <help>
142 <![CDATA[ 146 <![CDATA[
143 147
144 @MOTHUR_OVERVIEW@ 148 @MOTHUR_OVERVIEW@
145 149
146 **Command Documenation** 150 **Command Documentation**
147 151
148 The screen.seqs_ command enables you to keep sequences that fulfill certain user defined criteria. Furthermore, it enables you to cull those sequences not meeting the criteria from a name_, group_, or align.report_ file. 152 The screen.seqs_ command enables you to keep sequences that fulfill certain user defined criteria. Furthermore, it enables you to cull those sequences not meeting the criteria from a name_, group_, or align.report_ file.
149 153
150 .. _name: http://www.mothur.org/wiki/Name_file 154 .. _name: https://www.mothur.org/wiki/Name_file
151 .. _group: http://www.mothur.org/wiki/Group_file 155 .. _group: https://www.mothur.org/wiki/Group_file
152 .. _align.report: http://www.mothur.org/wiki/Align.seqs 156 .. _align.report: https://www.mothur.org/wiki/Align.seqs
153 .. _screen.seqs: http://www.mothur.org/wiki/Screen.seqs 157 .. _screen.seqs: https://www.mothur.org/wiki/Screen.seqs
154 158
155 ]]> 159 ]]>
156 </help> 160 </help>
157 <expand macro="citations"/> 161 <expand macro="citations"/>
158 </tool> 162 </tool>