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comparison meme_chip_wrapper.xml @ 9:89eab5bd597e draft default tip

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planemo upload
author eduardo
date Mon, 20 Feb 2017 14:02:55 -0500
parents 9fa889764fa5
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8:9fa889764fa5 9:89eab5bd597e
3 <requirement type="package" version="4.8.0">meme</requirement> 3 <requirement type="package" version="4.8.0">meme</requirement>
4 <requirement type="package" version="2.6">perl_module_HTML_Template</requirement> 4 <requirement type="package" version="2.6">perl_module_HTML_Template</requirement>
5 </requirements> 5 </requirements>
6 <description></description> 6 <description></description>
7 <version_command>echo "MEME version r4.10.0"</version_command> 7 <version_command>echo "MEME version r4.10.0"</version_command>
8 <command> meme-chip $input_file -o ${memechip_out.files_path} 8 <command> meme-chip $input_file -o ${html_outfile.files_path}
9 -db $__tool_directory__/JASPAR_CORE_2016.meme 9 -db $__tool_directory__/JASPAR_CORE_2016.meme
10 #if str( $options_type.options_type_selector ) == 'advanced': 10 #if str( $options_type.options_type_selector ) == 'advanced':
11 #if str( $options_type.bg_type.bg_type_selector) == 'bg_user': 11 #if str( $options_type.bg_type.bg_type_selector) == 'bg_user':
12 -bfile "${ str( $options_type.bg_type.bfile ) }" 12 -bfile "${ str( $options_type.bg_type.bfile ) }"
13 #end if 13 #end if
75 #end if 75 #end if
76 76
77 #end if 77 #end if
78 <!--pipe stderr to stdout because of annoying log4perl warnings. Error when exit status--> 78 <!--pipe stderr to stdout because of annoying log4perl warnings. Error when exit status-->
79 2&gt;&amp;1 || echo "Error running MEME." 79 2&gt;&amp;1 || echo "Error running MEME."
80 <!--&amp;&amp; mv ${html_outfile.files_path}/index.html ${html_outfile}--> 80 &amp;&amp; mv ${html_outfile.files_path}/index.html ${html_outfile}
81 <!--&amp;&amp; zip -r result $html_outfile.files_path--> 81 &amp;&amp; zip -r result $html_outfile.files_path
82 &amp;&amp; cd ${memechip_out.files_path} 82 <!--&amp;&amp; cd ${memechip_out.files_path}
83 &amp;&amp; zip -rp memechip_out ./ 83 &amp;&amp; zip -rp memechip_out ./
84 &amp;&amp; mv memechip_out.zip ${memechip_out} 84 &amp;&amp; mv memechip_out.zip ${memechip_out}-->
85 </command> 85 </command>
86 <inputs> 86 <inputs>
87 <param format="fasta" name="input_file" type="data" label="Sequences in fasta format" /> 87 <param format="fasta" name="input_file" type="data" label="Sequences in fasta format" />
88 <param name="motif_dbs" label="MEME Motif databases" type="select" multiple="true" display="checkboxes" help="Use CTRL to select multiple databases"> 88 <param name="motif_dbs" label="MEME Motif databases" type="select" multiple="true" display="checkboxes" help="Use CTRL to select multiple databases">
89 <options from_data_table="meme_chip_motifs"> 89 <options from_data_table="meme_chip_motifs">
156 156
157 </when> 157 </when>
158 </conditional> 158 </conditional>
159 </inputs> 159 </inputs>
160 <outputs> 160 <outputs>
161 <!--<data format="html" name="html_outfile" label="index" />--> 161 <data format="html" name="html_outfile" label="index" />
162 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />--> 162 <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
163 <data format="zip" name="memechip_out" label="SAVE ME ${tool.name} on #echo os.path.splitext(str($input_file.name))[0]#.zip" /> 163 <!--<data format="zip" name="memechip_out" label="SAVE ME ${tool.name} on #echo os.path.splitext(str($input_file.name))[0]#.zip" />-->
164 </outputs> 164 </outputs>
165 165
166 166
167 <tests> 167 <tests>
168 <test> 168 <test>