Mercurial > repos > iuc > meme_dreme

comparison dreme.xml @ 1:a154fa30afd1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
author iuc
date Thu, 17 May 2018 14:10:10 -0400
parents 315f05ef7d49
children f9553eb64650
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0:315f05ef7d49 1:a154fa30afd1
1 <tool id="meme_dreme" name="DREME" version="@WRAPPER_VERSION@.0"> 1 <tool id="meme_dreme" name="DREME" version="@WRAPPER_VERSION@.0">
2 <description>- Discriminative Regular Expression Motif Elicitation</description> 2 <description>- Discriminative Regular Expression Motif Elicitation</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 <requirement type="package" version="2.7">python</requirement>
8 </expand>
7 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
8 dreme 10 dreme
9 -o ./dreme_out 11 -o ./dreme_out
10 -p '$pos_fasta_file' 12 -p '$pos_fasta_file'
11 $norc 13 $norc
97 <test> 99 <test>
98 <param name="pos_fasta_file" value="dreme_test_sites.fa" ftype="fasta"/> 100 <param name="pos_fasta_file" value="dreme_test_sites.fa" ftype="fasta"/>
99 <param name="alphabet_type" value="-rna"/> 101 <param name="alphabet_type" value="-rna"/>
100 <param name="norc" value="false"/> 102 <param name="norc" value="false"/>
101 <param name="non_commercial_use" value="True"/> 103 <param name="non_commercial_use" value="True"/>
102 <output name="html_outfile" file="dreme1.html" lines_diff="16"/> 104 <output name="html_outfile" file="dreme_output_test1.html" lines_diff="22"/>
103 <output name="txt_outfile" file="dreme1.txt" lines_diff="22"/> 105 <output name="txt_outfile" file="dreme_output_test1.txt" lines_diff="22"/>
106 <output name="xml_outfile" file="dreme_output_test1.xml" lines_diff="22"/>
104 </test> 107 </test>
105 <test> 108 <test>
106 <param name="pos_fasta_file" value="dreme_test_sites.fa" ftype="fasta"/> 109 <param name="pos_fasta_file" value="dreme_test_sites.fa" ftype="fasta"/>
107 <param name="alphabet_type" value="-rna"/> 110 <param name="alphabet_type" value="-rna"/>
108 <param name="norc" value="false"/> 111 <param name="norc" value="false"/>
109 <param name="options_type_selector" value="advanced"/> 112 <param name="options_type_selector" value="advanced"/>
110 <param name="e_value_thr" value="0.00001"/> 113 <param name="e_value_thr" value="0.00001"/>
111 <param name="motif_min_k" value="4"/> 114 <param name="motif_min_k" value="4"/>
112 <param name="motif_max_k" value="10"/> 115 <param name="motif_max_k" value="10"/>
113 <param name="non_commercial_use" value="True"/> 116 <param name="non_commercial_use" value="True"/>
114 <output name="html_outfile" file="dreme2.html" lines_diff="29"/> 117 <output name="html_outfile" file="dreme_output_test2.html" lines_diff="22"/>
115 <output name="txt_outfile" file="dreme2.txt" lines_diff="29"/> 118 <output name="txt_outfile" file="dreme_output_test2.txt" lines_diff="22"/>
119 <output name="xml_outfile" file="dreme_output_test2.xml" lines_diff="22"/>
116 </test> 120 </test>
117 </tests> 121 </tests>
118 <help><![CDATA[ 122 <help><![CDATA[
119 DREME (Discriminative Regular Expression Motif Elicitation) discovers short, ungapped motifs (recurring, fixed-length patterns) that are relatively enriched in your sequences compared with shuffled sequences or given control sequences. 123 DREME (Discriminative Regular Expression Motif Elicitation) discovers short, ungapped motifs (recurring, fixed-length patterns) that are relatively enriched in your sequences compared with shuffled sequences or given control sequences.
120 124