Mercurial > repos > greg > meme_fimo
comparison fimo.xml @ 4:1f221102ac4d draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 16 Jun 2016 08:06:53 -0400 |
| parents | 09098f34f445 |
| children | 4df8e9f58a53 |
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| 3:ce656b846c8e | 4:1f221102ac4d |
|---|---|
| 31 #end if | 31 #end if |
| 32 --output_separate_motifs ${options_type.output_separate_motifs} | 32 --output_separate_motifs ${options_type.output_separate_motifs} |
| 33 --motif_pseudo "${options_type.motif_pseudo}" | 33 --motif_pseudo "${options_type.motif_pseudo}" |
| 34 ${options_type.no_qvalue} | 34 ${options_type.no_qvalue} |
| 35 ${options_type.norc} | 35 ${options_type.norc} |
| 36 ${options_type.parse_genomic_coord_cond.parse_genomic_coord} | 36 #if str($options_type.parse_genomic_coord_cond.parse_genomic_coord) == 'yes': |
| 37 #if str($options_type.parse_genomic_coord_cond.parse_genomic_coord) == '--parse_genomic_coord': | 37 --parse_genomic_coord 'yes' |
| 38 --remove_duplicate_coords ${options_type.parse_genomic_coord_cond.remove_duplicate_coords} | 38 --remove_duplicate_coords ${options_type.parse_genomic_coord_cond.remove_duplicate_coords} |
| 39 #end if | 39 #end if |
| 40 #if str($options_type.psp_cond.psp_selector) == 'yes': | 40 #if str($options_type.psp_cond.psp_selector) == 'yes': |
| 41 --input_psp "${input_psp}" | 41 --input_psp "${input_psp}" |
| 42 #end if | 42 #end if |
| 110 </param> | 110 </param> |
| 111 <param name="motif_pseudo" type="float" value="0.1" label="Pseudocount to add to counts in motif matrix" help="A pseudocount to be added to each count in the motif matrix, after first multiplying by the corresponding background frequency"/> | 111 <param name="motif_pseudo" type="float" value="0.1" label="Pseudocount to add to counts in motif matrix" help="A pseudocount to be added to each count in the motif matrix, after first multiplying by the corresponding background frequency"/> |
| 112 <param name="no_qvalue" label="Do not compute a q-value for each p-value" type="boolean" truevalue="--no_qvalue" falsevalue="" checked="True" help="The q-value calculation is that of Benjamini and Hochberg (1995)."/> | 112 <param name="no_qvalue" label="Do not compute a q-value for each p-value" type="boolean" truevalue="--no_qvalue" falsevalue="" checked="True" help="The q-value calculation is that of Benjamini and Hochberg (1995)."/> |
| 113 <param name="norc" label="Do not score the reverse complement DNA strand" type="boolean" truevalue="--norc" falsevalue="" checked="False" /> | 113 <param name="norc" label="Do not score the reverse complement DNA strand" type="boolean" truevalue="--norc" falsevalue="" checked="False" /> |
| 114 <conditional name="parse_genomic_coord_cond"> | 114 <conditional name="parse_genomic_coord_cond"> |
| 115 <param name="parse_genomic_coord" label="Check each sequence header for UCSC style genomic coordinates" type="boolean" truevalue="--parse_genomic_coord" falsevalue="" checked="False" /> | 115 <param name="parse_genomic_coord" label="Check each sequence header for UCSC style genomic coordinates" type="select"> |
| 116 <when value="--parse_genomic_coord"> | 116 <option value="no" selected="true">No</option> |
| 117 <param name="remove_duplicate_coords" type="select" label="Remove duplicate entries in unique GFF coordinates?" help="Remove duplicate entries as defined by the unique GFF coordinates"> | 117 <option value="yes">Yes</option> |
| 118 <option value="no" selected="true">No</option> | 118 </param> |
| 119 <option value="yes">Yes</option> | 119 <when value="yes"> |
| 120 </param> | 120 <param name="remove_duplicate_coords" type="boolean" truevalue="yes" falsevalue="no" label="Remove duplicate entries in unique GFF coordinates?" help="Remove duplicate entries as defined by the unique GFF coordinates" /> |
| 121 </when> | 121 </when> |
| 122 <when value=""/> | 122 <when value="no"/> |
| 123 </conditional> | 123 </conditional> |
| 124 <conditional name="psp_cond"> | 124 <conditional name="psp_cond"> |
| 125 <param name="psp_selector" type="select" label="Use position-specific priors?"> | 125 <param name="psp_selector" type="select" label="Use position-specific priors?"> |
| 126 <option value="no" selected="true">No</option> | 126 <option value="no" selected="true">No</option> |
| 127 <option value="yes">Yes</option> | 127 <option value="yes">Yes</option> |
| 230 <param name="options_type_selector" value="basic"/> | 230 <param name="options_type_selector" value="basic"/> |
| 231 <param name="non_commercial_use" value="True"/> | 231 <param name="non_commercial_use" value="True"/> |
| 232 <output name="html_outfile" file="fimo_output_html_1.html" compare="contains"/> | 232 <output name="html_outfile" file="fimo_output_html_1.html" compare="contains"/> |
| 233 <output name="txt_outfile" file="fimo_output_txt_1.txt" compare="contains"/> | 233 <output name="txt_outfile" file="fimo_output_txt_1.txt" compare="contains"/> |
| 234 <output name="gff_outfile" file="fimo_output_almost-gff_1.txt" compare="contains"/> | 234 <output name="gff_outfile" file="fimo_output_almost-gff_1.txt" compare="contains"/> |
| 235 <output name="xml_outfile" file="fimo_output_xml_1.xml" lines_diff="8"/> | 235 <output name="xml_outfile" file="fimo_output_xml_1.xml" compare="contains"/> |
| 236 <output name="interval_outfile" file="fimo_output_interval_1.txt" compare="contains"/> | 236 <output name="interval_outfile" file="fimo_output_interval_1.txt" compare="contains"/> |
| 237 </test> | 237 </test> |
| 238 <test> | 238 <test> |
| 239 <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/> | 239 <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/> |
| 240 <param name="fasta_type_selector" value="history"/> | 240 <param name="fasta_type_selector" value="history"/> |
| 242 <param name="options_type_selector" value="advanced"/> | 242 <param name="options_type_selector" value="advanced"/> |
| 243 <param name="non_commercial_use" value="True"/> | 243 <param name="non_commercial_use" value="True"/> |
| 244 <output name="html_outfile" file="fimo_output_html_2.html" compare="contains"/> | 244 <output name="html_outfile" file="fimo_output_html_2.html" compare="contains"/> |
| 245 <output name="txt_outfile" file="fimo_output_txt_2.txt" compare="contains"/> | 245 <output name="txt_outfile" file="fimo_output_txt_2.txt" compare="contains"/> |
| 246 <output name="gff_outfile" file="fimo_output_almost-gff_2.txt" compare="contains"/> | 246 <output name="gff_outfile" file="fimo_output_almost-gff_2.txt" compare="contains"/> |
| 247 <output name="xml_outfile" file="fimo_output_xml_2.xml" lines_diff="8"/> | 247 <output name="xml_outfile" file="fimo_output_xml_2.xml" compare="contains"/> |
| 248 <output name="interval_outfile" file="fimo_output_interval_2.txt" compare="contains"/> | 248 <output name="interval_outfile" file="fimo_output_interval_2.txt" compare="contains"/> |
| 249 </test> | 249 </test> |
| 250 <test> | 250 <test> |
| 251 <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/> | 251 <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/> |
| 252 <param name="fasta_type_selector" value="history"/> | 252 <param name="fasta_type_selector" value="history"/> |
| 257 <param name="output_separate_motifs" value="yes"/> | 257 <param name="output_separate_motifs" value="yes"/> |
| 258 <param name="non_commercial_use" value="True"/> | 258 <param name="non_commercial_use" value="True"/> |
| 259 <output name="html_outfile" file="fimo_output_html_2.html" compare="contains"/> | 259 <output name="html_outfile" file="fimo_output_html_2.html" compare="contains"/> |
| 260 <output name="txt_outfile" file="fimo_output_txt_2.txt" compare="contains"/> | 260 <output name="txt_outfile" file="fimo_output_txt_2.txt" compare="contains"/> |
| 261 <output_collection name="motifs" type="list"> | 261 <output_collection name="motifs" type="list"> |
| 262 <element name="MOTIFS1.gff" file="fimo_output_almost-gff_2.txt" ftype="gff" compare="contains"/> | 262 <element name="MOTIF1.gff" file="motif1.gff" ftype="gff" compare="contains"/> |
| 263 </output_collection> | 263 </output_collection> |
| 264 <output name="xml_outfile" file="fimo_output_xml_2.xml" lines_diff="8"/> | 264 <output name="xml_outfile" file="fimo_output_xml_2.xml" compare="contains"/> |
| 265 <output name="interval_outfile" file="fimo_output_interval_2.txt" compare="contains"/> | 265 <output name="interval_outfile" file="fimo_output_interval_2.txt" compare="contains"/> |
| 266 </test> | 266 </test> |
| 267 </tests> | 267 </tests> |
| 268 <help> | 268 <help> |
| 269 | 269 |