Mercurial > repos > iuc > mothur_sort_seqs

comparison sort.seqs.xml @ 5:805e64a3ef00 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 38a2bbee32eaaceeb22d7549b13dbc0c613ee173
author iuc
date Tue, 20 Mar 2018 13:44:58 -0400
parents af77b7eda3ce
children
comparison
equal deleted inserted replaced
4:1ea5114af11c 5:805e64a3ef00
58 <param name="name_in" type="data" format="mothur.names" optional="true" label="names - name reference" help="format must be mothur.names"/> 58 <param name="name_in" type="data" format="mothur.names" optional="true" label="names - name reference" help="format must be mothur.names"/>
59 <param name="tax_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - taxonomy reference" help="format must be mothur.seq.taxonomy"/> 59 <param name="tax_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - taxonomy reference" help="format must be mothur.seq.taxonomy"/>
60 <param name="accnos" type="data" format="mothur.accnos" optional="true" label="accnos - sort" help="format must be mothur.accnos"/> 60 <param name="accnos" type="data" format="mothur.accnos" optional="true" label="accnos - sort" help="format must be mothur.accnos"/>
61 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="format must be mothur.count_table (generated by count.seqs)"/> 61 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="format must be mothur.count_table (generated by count.seqs)"/>
62 <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Datasets are large and may not fit in RAM"/> 62 <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Datasets are large and may not fit in RAM"/>
63 <expand macro="param-savelog"/>
63 </inputs> 64 </inputs>
64 <outputs> 65 <outputs>
65 <expand macro="logfile-output"/> 66 <expand macro="logfile-output"/>
66 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.fasta"> 67 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.fasta">
67 <filter>fasta_in</filter> 68 <filter>fasta_in</filter>
84 </outputs> 85 </outputs>
85 <tests> 86 <tests>
86 <test> 87 <test>
87 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/> 88 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
88 <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/> 89 <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/>
90 <param name="savelog" value="true"/>
89 <expand macro="logfile-test"/> 91 <expand macro="logfile-test"/>
90 </test> 92 </test>
91 <test> 93 <test>
92 <param name="qfile_in" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/> 94 <param name="qfile_in" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/>
93 <output name="qfile_out" md5="abed9d1811786c810a12fd00a376cee4" ftype="qual454"/> 95 <output name="qfile_out" md5="abed9d1811786c810a12fd00a376cee4" ftype="qual454"/>
96 <param name="savelog" value="true"/>
94 <expand macro="logfile-test"/> 97 <expand macro="logfile-test"/>
95 </test> 98 </test>
96 <test> 99 <test>
97 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/> 100 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
98 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/> 101 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
102 <param name="savelog" value="true"/>
99 <expand macro="logfile-test"/> 103 <expand macro="logfile-test"/>
100 </test> 104 </test>
101 <test> 105 <test>
102 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/> 106 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
103 <param name="count" value="amazon.count_table" ftype="mothur.count_table"/> 107 <param name="count" value="amazon.count_table" ftype="mothur.count_table"/>
104 <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/> 108 <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/>
109 <param name="savelog" value="true"/>
105 <expand macro="logfile-test"/> 110 <expand macro="logfile-test"/>
106 </test> 111 </test>
107 <test><!-- test with multiple file types input --> 112 <test><!-- test with multiple file types input -->
108 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/> 113 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
109 <param name="qfile_in" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/> 114 <param name="qfile_in" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/>
110 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/> 115 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
111 <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/> 116 <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/>
112 <output name="qfile_out" md5="abed9d1811786c810a12fd00a376cee4" ftype="qual454"/> 117 <output name="qfile_out" md5="abed9d1811786c810a12fd00a376cee4" ftype="qual454"/>
113 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/> 118 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
119 <param name="savelog" value="true"/>
114 <expand macro="logfile-test"/> 120 <expand macro="logfile-test"/>
115 </test> 121 </test>
116 </tests> 122 </tests>
117 <help><![CDATA[ 123 <help><![CDATA[
118 124