meme_meme: meme.xml annotate

annotate meme.xml @ 10:b8c05adb68da draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e

author	iuc
date	Wed, 23 Aug 2017 20:57:09 -0400
parents	794b2859c286
children	7a5164f99316

rev	line source
10 b8c05adb68da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e iuc parents: 9 diff changeset	1 <tool id="meme_meme" name="MEME" version="@WRAPPER_VERSION@.0">
0 e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	2 <description>- Multiple Em for Motif Elicitation</description>
9 794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	3 <macros>
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	4 <import>macros.xml</import>
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	5 </macros>
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	6 <expand macro="requirements" />
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	7 <command detect_errors="exit_code"><![CDATA[
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	8 meme '$input1'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	9 -o '${html_outfile.files_path}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	10 -nostatus
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	11 -maxsize 1000000
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	12 #if str( $options_type.options_type_selector ) == 'advanced':
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	13 -sf '${ str( $options_type.sf ).replace( " ", "_" ) }'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	14 -${options_type.alphabet_type.alphabet_type_selector}
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	15 -mod '${options_type.mod_type.mod_type_selector}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	16 -nmotifs '${options_type.nmotifs}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	17 -wnsites '${options_type.wnsites}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	18 #if $options_type.evt < float('inf'):
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	19 -evt '${options_type.evt}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	20 #end if
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	21 #if str( $options_type.mod_type.mod_type_selector ) != 'oops':
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	22 #if str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'nsites':
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	23 -nsites '${options_type.mod_type.motif_occurrence_type.nsites}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	24 #elif str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'min_max_sites':
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	25 -minsites '${options_type.mod_type.motif_occurrence_type.minsites}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	26 -maxsites '${options_type.mod_type.motif_occurrence_type.maxsites}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	27 #end if
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	28 #end if
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	29 #if str( $options_type.motif_width_type.motif_width_type_selector ) == 'exact':
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	30 -w '${options_type.motif_width_type.width}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	31 #else
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	32 -minw '${options_type.motif_width_type.minw}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	33 -maxw '${options_type.motif_width_type.maxw}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	34 #end if
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	35 #if str( $options_type.motif_trim_type.motif_trim_type_selector ) == 'nomatrim':
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	36 -nomatrim
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	37 #else
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	38 -wg '${options_type.motif_trim_type.wg}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	39 -ws '${options_type.motif_trim_type.ws}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	40 ${options_type.motif_trim_type.noendgaps}
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	41 #end if
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	42 #if str( $options_type.bfile ) != 'None':
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	43 -bfile '${options_type.bfile}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	44 #end if
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	45 #if str( $options_type.pspfile ) != 'None':
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	46 -psp '${options_type.pspfile}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	47 #end if
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	48 #if str( $options_type.alphabet_type.alphabet_type_selector ) == 'dna':
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	49 ${options_type.alphabet_type.revcomp} ${options_type.alphabet_type.pal}
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	50 #end if
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	51 -maxiter '${options_type.maxiter}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	52 -distance '${options_type.distance}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	53 -prior '${options_type.alphabet_type.prior_type.prior_type_selector}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	54 #if str( $options_type.alphabet_type.prior_type.prior_type_selector ) != 'addone':
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	55 -b '${options_type.alphabet_type.prior_type.prior_b}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	56 #if str( $options_type.alphabet_type.prior_type.plib ) != 'None':
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	57 -plib '${options_type.alphabet_type.prior_type.plib}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	58 #end if
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	59 #end if
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	60 #if str( $options_type.alphabet_type.spmap_type.spmap_type_selector ) == 'cons':
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	61 -cons '${options_type.alphabet_type.spmap_type.cons}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	62 #else
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	63 -spmap '${options_type.alphabet_type.spmap_type.spmap_type_selector}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	64 -spfuzz '${options_type.alphabet_type.spmap_type.spfuzz}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	65 #end if
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	66 #if str( $options_type.branching_type.branching_type_selector ) == 'x_branch':
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	67 -x_branch
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	68 -bfactor '${options_type.branching_type.bfactor}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	69 -heapsize '${options_type.branching_type.heapsize}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	70 #end if
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	71 #end if
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	72 && mv '${html_outfile.files_path}/meme.html' '${html_outfile}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	73 && mv '${html_outfile.files_path}/meme.txt' '${txt_outfile}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	74 && mv '${html_outfile.files_path}/meme.xml' '${xml_outfile}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd iuc parents: 7 diff changeset	75 ]]></command>
0 e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	76 <inputs>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	77 <param format="fasta" name="input1" type="data" label="Sequences"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	78 <conditional name="options_type">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	79 <param name="options_type_selector" type="select" label="Options Configuration">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	80 <option value="basic" selected="true">Basic</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	81 <option value="advanced">Advanced</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	82 </param>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	83 <when value="basic" />
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	84 <when value="advanced">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	85 <param name="sf" type="text" value="Galaxy FASTA Input" label="Name of sequence set" argument="-sf"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	86 <conditional name="alphabet_type">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	87 <param name="alphabet_type_selector" type="select" label="Sequence Alphabet">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	88 <option value="protein">Protein</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	89 <option value="dna" selected="true">DNA</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	90 </param>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	91 <when value="protein">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	92 <conditional name="prior_type">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	93 <param name="prior_type_selector" type="select" label="Choice of prior" argument="-prior">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	94 <option value="dirichlet">simple Dirichlet prior</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	95 <option value="dmix" selected="true">mixture of Dirichlets prior</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	96 <option value="mega">extremely low variance dmix</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	97 <option value="megap">mega for all but last iteration of EM; dmix on last iteration</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	98 <option value="addone">add +1 to each observed count</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	99 </param>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	100 <when value="dirichlet">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	101 <param name="prior_b" type="float" value="0.01" label="strength of prior on model parameters" argument="-b"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	102 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	103 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	104 <when value="dmix">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	105 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	106 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	107 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	108 <when value="mega">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	109 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	110 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	111 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	112 <when value="megap">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	113 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	114 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	115 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	116 <when value="addone" />
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	117 </conditional>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	118 <conditional name="spmap_type">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	119 <param name="spmap_type_selector" type="select" label="EM starting points" argument="-spmap">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	120 <option value="uni">uni</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	121 <option value="pam" selected="true">pam</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	122 <option value="cons">Use starting point from string</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	123 </param>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	124 <when value="uni">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	125 <param name="spfuzz" type="float" value="0.5" label="Fuzziness of the mapping" argument="-spfuzz"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	126 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	127 <when value="pam">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	128 <param name="spfuzz" type="integer" value="120" label="Fuzziness of the mapping" argument="-spfuzz"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	129 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	130 <when value="cons">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	131 <param name="cons" type="text" value="" label="Starting point from string" argument="-cons"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	132 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	133 </conditional>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	134 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	135 <when value="dna">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	136 <param name="revcomp" label="Check reverse complement" type="boolean" truevalue="-revcomp" falsevalue="" checked="False"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	137 <param name="pal" label="Check for palindromes" type="boolean" truevalue="-pal" falsevalue="" checked="False"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	138 <conditional name="prior_type">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	139 <param name="prior_type_selector" type="select" label="Sequence Alphabet" argument="-prior">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	140 <option value="dirichlet" selected="true">simple Dirichlet prior</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	141 <option value="dmix">mixture of Dirichlets prior</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	142 <option value="mega">extremely low variance dmix</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	143 <option value="megap">mega for all but last iteration of EM; dmix on last iteration</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	144 <option value="addone">add +1 to each observed count</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	145 </param>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	146 <when value="dirichlet">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	147 <param name="prior_b" type="float" value="0.01" label="strength of prior on model parameters" argument="-b"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	148 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	149 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	150 <when value="dmix">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	151 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	152 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	153 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	154 <when value="mega">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	155 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	156 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	157 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	158 <when value="megap">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	159 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	160 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	161 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	162 <when value="addone" />
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	163 </conditional>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	164 <conditional name="spmap_type">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	165 <param name="spmap_type_selector" type="select" label="EM starting points" argument="-spmap">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	166 <option value="uni" selected="true">uni</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	167 <option value="pam">pam</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	168 <option value="cons">Use starting point from string</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	169 </param>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	170 <when value="uni">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	171 <param name="spfuzz" type="float" value="0.5" label="Fuzziness of the mapping" argument="-spfuzz"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	172 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	173 <when value="pam">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	174 <param name="spfuzz" type="integer" value="120" label="Fuzziness of the mapping" argument="-spfuzz"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	175 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	176 <when value="cons">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	177 <param name="cons" type="text" value="" label="Starting point from string" argument="-cons"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	178 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	179 </conditional>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	180 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	181 </conditional>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	182 <param name="nmotifs" type="integer" value="1" label="Number of different motifs to search" argument="-nmotifs" />
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	183 <param name="evt" type="float" value="inf" label="E-value to stop looking for motifs" argument="-evt"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	184 <conditional name="mod_type">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	185 <param name="mod_type_selector" type="select" label="Expected motif distribution" argument="-mod">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	186 <option value="oops">One Occurrence Per Sequence</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	187 <option value="zoops" selected="true">Zero or One Occurrence Per Sequence</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	188 <option value="anr">Any Number of Repetitions</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	189 </param>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	190 <when value="oops" />
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	191 <when value="zoops">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	192 <conditional name="motif_occurrence_type">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	193 <param name="motif_occurrence_type_selector" type="select" label="Number of motif occurrences">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	194 <option value="default" selected="true">Use defaults</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	195 <option value="nsites">nsites</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	196 <option value="min_max_sites">min and max sites</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	197 </param>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	198 <when value="default" />
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	199 <when value="nsites">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	200 <param name="nsites" type="integer" value="1" label="Search nsites number of occurrences" argument="-nsites"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	201 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	202 <when value="min_max_sites">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	203 <param name="minsites" type="integer" value="1" label="minsites" argument="-minsites"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	204 <param name="maxsites" type="integer" value="50" label="maxsites" argument="-maxsites"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	205 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	206 </conditional>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	207 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	208 <when value="anr">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	209 <conditional name="motif_occurrence_type">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	210 <param name="motif_occurrence_type_selector" type="select" label="Number of motif occurrences">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	211 <option value="default" selected="true">Use defaults</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	212 <option value="nsites">nsites</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	213 <option value="min_max_sites">min and max sites</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	214 </param>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	215 <when value="default" />
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	216 <when value="nsites">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	217 <param name="nsites" type="integer" value="1" label="Search nsites number of occurrences" argument="-nsites"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	218 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	219 <when value="min_max_sites">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	220 <param name="minsites" type="integer" value="1" label="minsites" argument="-minsites"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	221 <param name="maxsites" type="integer" value="50" label="maxsites" argument="-maxsites"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	222 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	223 </conditional>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	224 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	225 </conditional>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	226 <param name="wnsites" type="float" value="0.8" label="Weight on the prior on nsites" argument="-wnsites"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	227 <conditional name="motif_width_type">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	228 <param name="motif_width_type_selector" type="select" label="Motif width type">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	229 <option value="exact">Exact width</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	230 <option value="range" selected="true">Specify a range</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	231 </param>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	232 <when value="exact">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	233 <param name="width" type="integer" value="10" label="Width of motif to search" argument="-w"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	234 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	235 <when value="range">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	236 <param name="minw" type="integer" value="8" label="Min width of motif to search" argument="-minw"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	237 <param name="maxw" type="integer" value="50" label="Max width of motif to search" argument="-maxw"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	238 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	239 </conditional>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	240 <conditional name="motif_trim_type">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	241 <param name="motif_trim_type_selector" type="select" label="Motif trim type">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	242 <option value="nomatrim">No motif trim</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	243 <option value="trim" selected="true">Trim motif</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	244 </param>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	245 <when value="nomatrim" />
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	246 <when value="trim">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	247 <param name="wg" type="integer" value="11" label="Gap cost" argument="-wg"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	248 <param name="ws" type="integer" value="1" label="Space cost" argument="-ws"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	249 <param name="noendgaps" label="Do not penalize endgaps" type="boolean" truevalue="-noendgaps" falsevalue="" checked="False"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	250 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	251 </conditional>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	252 <param name="bfile" type="data" format="txt" optional="True" label="Background Model" argument="-bfile"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	253 <param name="pspfile" type="data" format="txt" optional="True" label="Position-Specific Prior" argument="-psp"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	254 <param name="maxiter" type="integer" value="50" label="Number of iterations of EM to run" argument="-maxiter"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	255 <param name="distance" type="float" value="0.001" label="Convergence criterion" argument="-distance"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	256 <conditional name="branching_type">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	257 <param name="branching_type_selector" type="select" label="x-branching type">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	258 <option value="x_branch">Perform x-branching</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	259 <option value="no_x_branch" selected="true">No x-branching</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	260 </param>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	261 <when value="no_x_branch" />
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	262 <when value="x_branch">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	263 <param name="bfactor" type="integer" value="3" label="Number of iterations of branching" argument="-bfactor"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	264 <param name="heapsize" type="integer" value="64" label="Maximum number of heaps to use" argument="-heapsize"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	265 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	266 </conditional>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	267 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	268 </conditional>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	269 <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">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	270 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	271 </param>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	272 </inputs>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	273 <outputs>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	274 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	275 <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (text)"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	276 <data format="memexml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	277 </outputs>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	278 <tests>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	279 <test>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	280 <param name="input1" value="meme_input_1.fasta" ftype="fasta" dbkey="hg19"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	281 <param name="options_type_selector" value="basic"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	282 <param name="non_commercial_use" value="True"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	283 <output name="html_outfile" file="meme_output_html_1.html" compare="contains"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	284 <output name="txt_outfile" file="meme_output_txt_1.txt" lines_diff="12"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	285 <output name="xml_outfile" file="meme_output_xml_1.xml" lines_diff="8"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	286 </test>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	287 <test>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	288 <param name="input1" value="meme_input_1.fasta" ftype="fasta" dbkey="hg19"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	289 <param name="options_type_selector" value="advanced"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	290 <param name="plib" value="prior30.plib" ftype="txt"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	291 <param name="non_commercial_use" value="True"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	292 <output name="html_outfile" file="meme_output_html_2.html" compare="contains"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	293 <output name="txt_outfile" file="meme_output_txt_2.txt" lines_diff="12"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	294 <output name="xml_outfile" file="meme_output_xml_2.xml" lines_diff="8"/>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	295 </test>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	296 </tests>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	297 <help>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	298
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	299 .. class:: warningmark
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	300
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	301 **WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted.
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	302 Before using, be sure to review, agree, and comply with the license.**
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	303
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	304 If you want to specify sequence weights, you must include them at the top of your input FASTA file.
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	305
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	306 MEME discovers novel, ungapped motifs (recurring, fixed-length patterns) in your sequences (sample output from sequences).
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	307 MEME splits variable-length patterns into two or more separate motifs. A motif is a sequence pattern that occurs repeatedly
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	308 in a group of related sequences. MEME represents motifs as position-dependent letter-probability matrices which describe the
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	309 probability of each possible letter at each position in the pattern. Individual MEME motifs do not contain gaps. Patterns
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	310 with variable-length gaps are split by MEME into two or more separate motifs. MEME takes as input a group of sequences and
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	311 outputs as many motifs as requested. MEME uses statistical modeling techniques to automatically choose the best width, number
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	312 of occurrences, and description for each motif.
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	313
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	314 .. class:: infomark
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	315
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	316 For detailed information on MEME, click here_, or view the license_.
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	317
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	318 .. _here: http://meme-suite.org/doc/meme.html?man_type=web
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	319 .. _license: http://meme-suite.org/doc/copyright.html?man_type=web
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	320
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	321 </help>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	322 <citations>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	323 <citation type="bibtex">
4 cc283f3e5863 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31 iuc parents: 2 diff changeset	324 @article{Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California,
0 e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	325 author = {Bailey,Timothy L. and Elkan, Charles},
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	326 title = {Fitting a mixture model by expectation maximization to discover motifs in biopolymers},
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	327 year = {1994},
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	328 eprint = {None},
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	329 url = {http://www.sdsc.edu/~tbailey/papers/ismb94.pdf}
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	330 }</citation>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	331 </citations>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1 iuc parents: diff changeset	332 </tool>

Mercurial > repos > iuc > meme_meme

annotate meme.xml @ 10:b8c05adb68da draft