meme_test: meme.xml annotate

annotate meme.xml @ 2:6b2d1988a579 draft default tip

planemo upload for repository http://meme-suite.org/tools/meme

author	mvdbeek
date	Thu, 28 May 2015 11:58:21 -0400
parents	d358e2bd1598
children

rev	line source
2 6b2d1988a579 planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: 1 diff changeset	1 <tool id="meme_meme" name="MEME" version="1.0.3">
0 838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	2 <requirements>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	3 <requirement type="package" version="4.10.0_4">meme</requirement>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	4 </requirements>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	5 <description>motif discovery</description>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	6 <command>meme "$input1" -o "${html_outfile.files_path}"
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	7 -nostatus
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	8
2 6b2d1988a579 planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: 1 diff changeset	9 ##-p \${GALAXY_SLOTS:-4} ##number of processors, but requires MPI.
0 838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	10
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	11 #if str( $options_type.options_type_selector ) == 'advanced':
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	12 -sf "${ str( $options_type.sf ).replace( ' ', '_' ) }"
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	13 -${options_type.alphabet_type.alphabet_type_selector}
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	14 -mod "${options_type.mod_type.mod_type_selector}"
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	15 -nmotifs "${options_type.nmotifs}"
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	16 -wnsites "${options_type.wnsites}"
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	17 -maxsize "${options_type.maxsize}"
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	18
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	19 #if $options_type.evt < float('inf'):
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	20 -evt "${options_type.evt}"
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	21 #end if
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	22
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	23 #if str( $options_type.mod_type.mod_type_selector ) != 'oops':
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	24 #if str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'nsites':
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	25 -nsites "${options_type.mod_type.motif_occurrence_type.nsites}"
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	26 #elif str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'min_max_sites':
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	27 -minsites "${options_type.mod_type.motif_occurrence_type.minsites}" -maxsites "${options_type.mod_type.motif_occurrence_type.maxsites}"
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	28 #end if
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	29 #end if
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	30
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	31 #if str( $options_type.motif_width_type.motif_width_type_selector ) == 'exact':
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	32 -w "${options_type.motif_width_type.width}"
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	33 #else
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	34 -minw "${options_type.motif_width_type.minw}" -maxw "${options_type.motif_width_type.maxw}"
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	35 #end if
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	36
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	37 #if str( $options_type.motif_trim_type.motif_trim_type_selector ) == 'nomatrim':
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	38 -nomatrim
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	39 #else
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	40 -wg "${options_type.motif_trim_type.wg}" -ws "${options_type.motif_trim_type.ws}" ${options_type.motif_trim_type.noendgaps}
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	41 #end if
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	42
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	43 #if str( $options_type.bfile ) != 'None':
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	44 -bfile "${options_type.bfile}"
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	45 #end if
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	46
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	47 #if str( $options_type.pspfile ) != 'None':
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	48 -psp "${options_type.pspfile}"
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	49 #end if
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	50
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	51 #if str( $options_type.alphabet_type.alphabet_type_selector ) == "dna":
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	52 ${options_type.alphabet_type.revcomp} ${options_type.alphabet_type.pal}
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	53 #end if
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	54
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	55 -maxiter "${options_type.maxiter}" -distance "${options_type.distance}"
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	56
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	57 -prior "${options_type.alphabet_type.prior_type.prior_type_selector}"
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	58 #if str( $options_type.alphabet_type.prior_type.prior_type_selector ) != 'addone':
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	59 -b "${options_type.alphabet_type.prior_type.prior_b}"
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	60 #if str( $options_type.alphabet_type.prior_type.plib ) != 'None':
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	61 -plib "${options_type.alphabet_type.prior_type.plib}"
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	62 #end if
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	63 #end if
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	64
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	65 #if str( $options_type.alphabet_type.spmap_type.spmap_type_selector ) == 'cons':
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	66 -cons "${options_type.alphabet_type.spmap_type.cons}"
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	67 #else
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	68 -spmap "${options_type.alphabet_type.spmap_type.spmap_type_selector}"
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	69 -spfuzz "${options_type.alphabet_type.spmap_type.spfuzz}"
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	70 #end if
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	71
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	72 #if str( $options_type.branching_type.branching_type_selector ) == 'x_branch':
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	73 -x_branch -bfactor "${options_type.branching_type.bfactor}" -heapsize "${options_type.branching_type.heapsize}"
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	74 #end if
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	75
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	76 ##-maxsize "1000000" ##remove hardcoded maxsize? should increase number of processors instead
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	77
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	78 #end if
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	79
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	80 2>&1 \|\| echo "Error running MEME."
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	81
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	82
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	83 && mv ${html_outfile.files_path}/meme.html ${html_outfile}
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	84
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	85 && mv ${html_outfile.files_path}/meme.txt ${txt_outfile}
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	86
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	87 && mv ${html_outfile.files_path}/meme.xml ${xml_outfile}
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	88
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	89 </command>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	90 <inputs>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	91 <param format="fasta" name="input1" type="data" label="Sequences"/>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	92
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	93 <conditional name="options_type">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	94 <param name="options_type_selector" type="select" label="Options Configuration">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	95 <option value="basic" selected="true">Basic</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	96 <option value="advanced">Advanced</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	97 </param>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	98 <when value="basic">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	99 <!-- do nothing here -->
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	100 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	101 <when value="advanced">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	102
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	103 <param name="sf" type="text" value="Galaxy FASTA Input" label="Name of sequence set" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	104
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	105 <conditional name="alphabet_type">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	106 <param name="alphabet_type_selector" type="select" label="Sequence Alphabet">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	107 <option value="protein">Protein</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	108 <option value="dna" selected="true">DNA</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	109 </param>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	110 <when value="protein">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	111 <conditional name="prior_type">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	112 <param name="prior_type_selector" type="select" label="Choice of prior">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	113 <option value="dirichlet">simple Dirichlet prior</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	114 <option value="dmix" selected="true">mixture of Dirichlets prior</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	115 <option value="mega">extremely low variance dmix</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	116 <option value="megap">mega for all but last iteration of EM; dmix on last iteration</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	117 <option value="addone">add +1 to each observed count</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	118 </param>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	119 <when value="dirichlet">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	120 <param name="prior_b" type="float" value="0.01" label="strength of prior on model parameters" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	121 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	122 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	123 <when value="dmix">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	124 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	125 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	126 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	127 <when value="mega">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	128 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	129 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	130 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	131 <when value="megap">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	132 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	133 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	134 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	135 <when value="addone">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	136 <!-- no values here? -->
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	137 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	138 </conditional>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	139 <conditional name="spmap_type">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	140 <param name="spmap_type_selector" type="select" label="EM starting points">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	141 <option value="uni">uni</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	142 <option value="pam" selected="true">pam</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	143 <option value="cons">Use starting point from string</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	144 </param>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	145 <when value="uni">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	146 <param name="spfuzz" type="float" value="0.5" label="Fuzziness of the mapping" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	147 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	148 <when value="pam">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	149 <param name="spfuzz" type="integer" value="120" label="Fuzziness of the mapping" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	150 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	151 <when value="cons">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	152 <param name="cons" type="text" value="" label="Starting point from string" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	153 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	154 </conditional>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	155 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	156 <when value="dna">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	157 <param name="revcomp" label="Check reverse complement" type="boolean" truevalue="-revcomp" falsevalue="" checked="False"/>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	158 <param name="pal" label="Check for palindromes" type="boolean" truevalue="-pal" falsevalue="" checked="False"/>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	159 <conditional name="prior_type">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	160 <param name="prior_type_selector" type="select" label="Sequence Alphabet">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	161 <option value="dirichlet" selected="true">simple Dirichlet prior</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	162 <option value="dmix">mixture of Dirichlets prior</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	163 <option value="mega">extremely low variance dmix</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	164 <option value="megap">mega for all but last iteration of EM; dmix on last iteration</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	165 <option value="addone">add +1 to each observed count</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	166 </param>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	167 <when value="dirichlet">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	168 <param name="prior_b" type="float" value="0.01" label="strength of prior on model parameters" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	169 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	170 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	171 <when value="dmix">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	172 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	173 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	174 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	175 <when value="mega">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	176 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	177 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	178 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	179 <when value="megap">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	180 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	181 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	182 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	183 <when value="addone">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	184 <!-- no values here? -->
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	185 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	186 </conditional>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	187 <conditional name="spmap_type">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	188 <param name="spmap_type_selector" type="select" label="EM starting points">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	189 <option value="uni" selected="true">uni</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	190 <option value="pam">pam</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	191 <option value="cons">Use starting point from string</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	192 </param>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	193 <when value="uni">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	194 <param name="spfuzz" type="float" value="0.5" label="Fuzziness of the mapping" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	195 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	196 <when value="pam">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	197 <param name="spfuzz" type="integer" value="120" label="Fuzziness of the mapping" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	198 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	199 <when value="cons">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	200 <param name="cons" type="text" value="" label="Starting point from string" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	201 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	202 </conditional>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	203 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	204 </conditional>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	205
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	206 <param name="nmotifs" type="integer" value="1" label="Number of different motifs to search" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	207 <param name="maxsize" type="integer" value="1000000" label="Max number of characters in the sequence file"/>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	208 <param name="evt" type="float" value="inf" label="E-value to stop looking for motifs" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	209 <conditional name="mod_type">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	210 <param name="mod_type_selector" type="select" label="Expected motif distribution">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	211 <option value="oops">One Occurrence Per Sequence</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	212 <option value="zoops" selected="true">Zero or One Occurrence Per Sequence</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	213 <option value="anr">Any Number of Repetitions</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	214 </param>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	215 <when value="oops">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	216 <!-- no values here -->
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	217 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	218 <when value="zoops">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	219 <conditional name="motif_occurrence_type">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	220 <param name="motif_occurrence_type_selector" type="select" label="Number of motif occurrences">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	221 <option value="default" selected="true">Use defaults</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	222 <option value="nsites">nsites</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	223 <option value="min_max_sites">min and max sites</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	224 </param>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	225 <when value="default">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	226 <!-- no values here -->
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	227 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	228 <when value="nsites">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	229 <param name="nsites" type="integer" value="1" label="Search nsites number of occurrences" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	230 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	231 <when value="min_max_sites">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	232 <param name="minsites" type="integer" value="1" label="minsites" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	233 <param name="maxsites" type="integer" value="50" label="maxsites" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	234 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	235 </conditional>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	236 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	237 <when value="anr">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	238 <conditional name="motif_occurrence_type">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	239 <param name="motif_occurrence_type_selector" type="select" label="Number of motif occurrences">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	240 <option value="default" selected="true">Use defaults</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	241 <option value="nsites">nsites</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	242 <option value="min_max_sites">min and max sites</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	243 </param>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	244 <when value="default">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	245 <!-- no values here -->
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	246 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	247 <when value="nsites">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	248 <param name="nsites" type="integer" value="1" label="Search nsites number of occurrences" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	249 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	250 <when value="min_max_sites">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	251 <param name="minsites" type="integer" value="1" label="minsites" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	252 <param name="maxsites" type="integer" value="50" label="maxsites" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	253 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	254 </conditional>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	255 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	256 </conditional>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	257 <param name="wnsites" type="float" value="0.8" label="Weight on the prior on nsites" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	258
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	259 <conditional name="motif_width_type">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	260 <param name="motif_width_type_selector" type="select" label="Motif width type">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	261 <option value="exact">Exact width</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	262 <option value="range" selected="true">Specify a range</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	263 </param>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	264 <when value="exact">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	265 <param name="width" type="integer" value="10" label="Width of motif to search" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	266 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	267 <when value="range">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	268 <param name="minw" type="integer" value="8" label="Min width of motif to search" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	269 <param name="maxw" type="integer" value="50" label="Max width of motif to search" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	270 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	271 </conditional>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	272
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	273 <conditional name="motif_trim_type">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	274 <param name="motif_trim_type_selector" type="select" label="Motif trim type">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	275 <option value="nomatrim">No motif trim</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	276 <option value="trim" selected="true">Trim motif</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	277 </param>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	278 <when value="nomatrim">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	279 <!-- no values here -->
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	280 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	281 <when value="trim">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	282 <param name="wg" type="integer" value="11" label="Gap cost" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	283 <param name="ws" type="integer" value="1" label="Space cost" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	284 <param name="noendgaps" label="Do not penalize endgaps" type="boolean" truevalue="-noendgaps" falsevalue="" checked="False"/>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	285 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	286 </conditional>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	287
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	288 <param name="bfile" type="data" format="txt" optional="True" label="Background Model" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	289 <param name="pspfile" type="data" format="txt" optional="True" label="Position-Specific Prior" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	290
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	291 <param name="maxiter" type="integer" value="50" label="Number of iterations of EM to run" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	292 <param name="distance" type="float" value="0.001" label="Convergence criterion" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	293
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	294 <conditional name="branching_type">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	295 <param name="branching_type_selector" type="select" label="x-branching type">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	296 <option value="x_branch">Perform x-branching</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	297 <option value="no_x_branch" selected="true">No x-branching</option>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	298 </param>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	299 <when value="no_x_branch">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	300 <!-- no values here -->
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	301 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	302 <when value="x_branch">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	303 <param name="bfactor" type="integer" value="3" label="Number of iterations of branching" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	304 <param name="heapsize" type="integer" value="64" label="Maximum number of heaps to use" />
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	305 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	306 </conditional>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	307
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	308 </when>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	309 </conditional>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	310
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	311 <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False">
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	312 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	313 </param>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	314
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	315 </inputs>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	316 <outputs>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	317 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"/>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	318 <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (text)"/>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	319 <data format="memexml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)"/>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	320 </outputs>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	321 <tests>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	322 <test>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	323 <param name="input1" value="meme/meme/meme_input_1.fasta" ftype="fasta" dbkey="hg19"/>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	324 <param name="options_type_selector" value="basic"/>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	325 <param name="non_commercial_use" value="True"/>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	326 <output name="html_outfile" file="meme/meme/meme_output_html_1.html" lines_diff="12"/>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	327 <output name="txt_outfile" file="meme/meme/meme_output_txt_1.txt" lines_diff="12"/>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	328 <output name="xml_outfile" file="meme/meme/meme_output_xml_1.xml" lines_diff="8"/>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	329 </test>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	330 </tests>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	331 <help>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	332
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	333 .. class:: warningmark
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	334
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	335 WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted. Before using, be sure to review, agree, and comply with the license.
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	336
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	337 If you want to specify sequence weights, you must include them at the top of your input FASTA file.
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	338
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	339 .. class:: infomark
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	340
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	341 To cite MEME:
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	342 Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994.
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	343
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	344
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	345 For detailed information on MEME, click here_. To view the license_.
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	346
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	347 .. _here: http://meme.nbcr.net/meme/meme-intro.html
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	348 .. _license: http://meme.nbcr.net/meme/COPYRIGHT.html
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	349
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	350 </help>
838fd0e0e13c planemo upload for repository http://meme-suite.org/tools/meme mvdbeek parents: diff changeset	351 </tool>

Mercurial > repos > mvdbeek > meme_test

annotate meme.xml @ 2:6b2d1988a579 draft default tip