Mercurial > repos > iuc > meme_meme

annotate meme.xml @ 19:7ce0fe11b411 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
author iuc
date Thu, 29 Aug 2024 10:20:10 +0000
parents 19237efe98d1
children
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19
7ce0fe11b411 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
1 <tool id="meme_meme" name="MEME" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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57e5d9382f36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents: 11
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2 <description>- Multiple EM for Motif Elicitation</description>
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7ce0fe11b411 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
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3 <macros>
7ce0fe11b411 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
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4 <import>macros.xml</import>
7ce0fe11b411 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
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5 </macros>
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3c2ac7c3f0b8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 8c1eac566cbcc93ceb3d753170bce144d386722c"
iuc
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6 <xrefs>
3c2ac7c3f0b8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 8c1eac566cbcc93ceb3d753170bce144d386722c"
iuc
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7 <xref type="bio.tools">meme_meme</xref>
3c2ac7c3f0b8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 8c1eac566cbcc93ceb3d753170bce144d386722c"
iuc
parents: 15
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8 </xrefs>
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7ce0fe11b411 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
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9 <expand macro="requirements"/>
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794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
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10 <command detect_errors="exit_code"><![CDATA[
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3c2ac7c3f0b8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 8c1eac566cbcc93ceb3d753170bce144d386722c"
iuc
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11 @CHECK_NON_COMMERCIAL_USE@
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9dd5373f6a5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
iuc
parents: 14
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12 export TMPDIR=\${TMPDIR:-.};
9dd5373f6a5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
iuc
parents: 14
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13
9
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
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14 meme '$input1'
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9dd5373f6a5a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
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15 -p \${GALAXY_SLOTS:-1}
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794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
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16 -o '${html_outfile.files_path}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
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17 -nostatus
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
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18 -maxsize 1000000
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
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19 #if str( $options_type.options_type_selector ) == 'advanced':
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
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20 -sf '${ str( $options_type.sf ).replace( " ", "_" ) }'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
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21 -${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
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22 -mod '${options_type.mod_type.mod_type_selector}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
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23 -nmotifs '${options_type.nmotifs}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
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24 -wnsites '${options_type.wnsites}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
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25 #if $options_type.evt < float('inf'):
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
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26 -evt '${options_type.evt}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
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27 #end if
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
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28 #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
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29 #if str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'nsites':
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
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30 -nsites '${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
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31 #elif str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'min_max_sites':
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
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32 -minsites '${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
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33 -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
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34 #end if
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
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35 #end if
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
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36 #if str( $options_type.motif_width_type.motif_width_type_selector ) == 'exact':
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
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37 -w '${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
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38 #else
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
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39 -minw '${options_type.motif_width_type.minw}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
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40 -maxw '${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
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41 #end if
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
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42 #if str( $options_type.motif_trim_type.motif_trim_type_selector ) == 'nomatrim':
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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43 -nomatrim
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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44 #else
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents: 7
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45 -wg '${options_type.motif_trim_type.wg}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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parents: 7
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46 -ws '${options_type.motif_trim_type.ws}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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47 ${options_type.motif_trim_type.noendgaps}
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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48 #end if
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
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49 #if str( $options_type.bfile ) != 'None':
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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50 -bfile '${options_type.bfile}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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51 #end if
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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52 #if str( $options_type.pspfile ) != 'None':
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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53 -psp '${options_type.pspfile}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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parents: 7
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54 #end if
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
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55 #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
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56 ${options_type.alphabet_type.revcomp} ${options_type.alphabet_type.pal}
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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57 #end if
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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58 -maxiter '${options_type.maxiter}'
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59 -distance '${options_type.distance}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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60 -prior '${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
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61 #if str( $options_type.alphabet_type.prior_type.prior_type_selector ) != 'addone':
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62 -b '${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
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63 #if str( $options_type.alphabet_type.prior_type.plib ) != 'None':
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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64 -plib '${options_type.alphabet_type.prior_type.plib}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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65 #end if
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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66 #end if
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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67 #if str( $options_type.alphabet_type.spmap_type.spmap_type_selector ) == 'cons':
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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68 -cons '${options_type.alphabet_type.spmap_type.cons}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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69 #else
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70 -spmap '${options_type.alphabet_type.spmap_type.spmap_type_selector}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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71 -spfuzz '${options_type.alphabet_type.spmap_type.spfuzz}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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72 #end if
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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73 #if str( $options_type.branching_type.branching_type_selector ) == 'x_branch':
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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74 -x_branch
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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75 -bfactor '${options_type.branching_type.bfactor}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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76 -heapsize '${options_type.branching_type.heapsize}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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77 #end if
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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78 #end if
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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79 && mv '${html_outfile.files_path}/meme.html' '${html_outfile}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
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80 && mv '${html_outfile.files_path}/meme.txt' '${txt_outfile}'
794b2859c286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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81 && mv '${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
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82 ]]></command>
0
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83 <inputs>
19
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84 <param name="input1" type="data" format="fasta" label="Sequences"/>
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85 <conditional name="options_type">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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diff changeset
86 <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:
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87 <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:
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88 <option value="advanced">Advanced</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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89 </param>
19
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parents: 18
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90 <when value="basic"/>
0
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iuc
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91 <when value="advanced">
19
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diff changeset
92 <param argument="-sf" type="text" value="Galaxy FASTA Input" label="Name of sequence set"/>
0
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iuc
parents:
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93 <conditional name="alphabet_type">
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
iuc
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94 <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:
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95 <option value="protein">Protein</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
iuc
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96 <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
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97 </param>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
iuc
parents:
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98 <when value="protein">
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iuc
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99 <conditional name="prior_type">
19
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100 <param name="prior_type_selector" argument="-prior" type="select" label="Choice of prior">
0
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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101 <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
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102 <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
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103 <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
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104 <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
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105 <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
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106 </param>
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iuc
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107 <when value="dirichlet">
19
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108 <param name="prior_b" argument="-b" type="float" value="0.01" label="strength of prior on model parameters"/>
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109 <param argument="-plib" type="data" format="txt" optional="True" label="Dirichlet prior file"/>
0
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110 </when>
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iuc
parents:
diff changeset
111 <when value="dmix">
19
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parents: 18
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112 <param name="prior_b" argument="-b" type="float" value="0" label="strength of prior on model parameters"/>
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113 <param argument="-plib" type="data" format="txt" optional="True" label="Dirichlet prior file"/>
0
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114 </when>
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iuc
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115 <when value="mega">
19
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parents: 18
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116 <param name="prior_b" argument="-b" type="float" value="0" label="strength of prior on model parameters"/>
7ce0fe11b411 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
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parents: 18
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117 <param argument="-plib" type="data" format="txt" optional="True" label="Dirichlet prior file"/>
0
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118 </when>
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iuc
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119 <when value="megap">
19
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parents: 18
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120 <param name="prior_b" argument="-b" type="float" value="0" label="strength of prior on model parameters"/>
7ce0fe11b411 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
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parents: 18
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121 <param argument="-plib" type="data" format="txt" optional="True" label="Dirichlet prior file"/>
0
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122 </when>
19
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iuc
parents: 18
diff changeset
123 <when value="addone"/>
0
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124 </conditional>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
iuc
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125 <conditional name="spmap_type">
19
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diff changeset
126 <param name="spmap_type_selector" argument="-spmap" type="select" label="EM starting points">
0
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
iuc
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127 <option value="uni">uni</option>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
iuc
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128 <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
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129 <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
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130 </param>
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iuc
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131 <when value="uni">
19
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132 <param argument="-spfuzz" type="float" value="0.5" label="Fuzziness of the mapping"/>
0
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133 </when>
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iuc
parents:
diff changeset
134 <when value="pam">
19
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parents: 18
diff changeset
135 <param argument="-spfuzz" type="integer" value="120" label="Fuzziness of the mapping"/>
0
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
iuc
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diff changeset
136 </when>
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iuc
parents:
diff changeset
137 <when value="cons">
19
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parents: 18
diff changeset
138 <param argument="-cons" type="text" value="" label="Starting point from string"/>
0
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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139 </when>
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iuc
parents:
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140 </conditional>
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141 </when>
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
iuc
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142 <when value="dna">
19
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parents: 18
diff changeset
143 <param argument="-revcomp" type="boolean" truevalue="-revcomp" falsevalue="" checked="False" label="Check reverse complement"/>
7ce0fe11b411 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
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144 <param argument="-pal" type="boolean" truevalue="-pal" falsevalue="" checked="False" label="Check for palindromes"/>
0
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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145 <conditional name="prior_type">
19
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146 <param name="prior_type_selector" argument="-prior" type="select" label="Sequence Alphabet">
0
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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147 <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
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148 <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
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149 <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
150 <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
151 <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
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diff changeset
152 </param>
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diff changeset
153 <when value="dirichlet">
19
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parents: 18
diff changeset
154 <param name="prior_b" argument="-b" type="float" value="0.01" label="strength of prior on model parameters"/>
7ce0fe11b411 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
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parents: 18
diff changeset
155 <param argument="-plib" type="data" format="txt" optional="True" label="Dirichlet prior file"/>
0
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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156 </when>
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iuc
parents:
diff changeset
157 <when value="dmix">
19
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158 <param name="prior_b" argument="-b" type="float" value="0" label="strength of prior on model parameters"/>
7ce0fe11b411 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
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parents: 18
diff changeset
159 <param argument="-plib" type="data" format="txt" optional="True" label="Dirichlet prior file"/>
0
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parents:
diff changeset
160 </when>
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iuc
parents:
diff changeset
161 <when value="mega">
19
7ce0fe11b411 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
162 <param name="prior_b" argument="-b" type="float" value="0" label="strength of prior on model parameters"/>
7ce0fe11b411 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
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parents: 18
diff changeset
163 <param argument="-plib" type="data" format="txt" optional="True" label="Dirichlet prior file"/>
0
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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diff changeset
164 </when>
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diff changeset
165 <when value="megap">
19
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parents: 18
diff changeset
166 <param name="prior_b" argument="-b" type="float" value="0" label="strength of prior on model parameters"/>
7ce0fe11b411 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
iuc
parents: 18
diff changeset
167 <param argument="-plib" type="data" format="txt" optional="True" label="Dirichlet prior file"/>
0
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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diff changeset
168 </when>
19
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parents: 18
diff changeset
169 <when value="addone"/>
0
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170 </conditional>
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iuc
parents:
diff changeset
171 <conditional name="spmap_type">
19
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iuc
parents: 18
diff changeset
172 <param name="spmap_type_selector" argument="-spmap" type="select" label="EM starting points">
0
e416c7c26977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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173 <option value="uni" selected="true">uni</option>
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174 <option value="pam">pam</option>
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175 <option value="cons">Use starting point from string</option>
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176 </param>
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177 <when value="uni">
19
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178 <param argument="-spfuzz" type="float" value="0.5" label="Fuzziness of the mapping"/>
0
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179 </when>
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180 <when value="pam">
19
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181 <param argument="-spfuzz" type="integer" value="120" label="Fuzziness of the mapping"/>
0
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182 </when>
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183 <when value="cons">
19
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184 <param argument="-cons" type="text" value="" label="Starting point from string"/>
0
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185 </when>
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186 </conditional>
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187 </when>
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188 </conditional>
19
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189 <param argument="-nmotifs" type="integer" value="1" label="Number of different motifs to search"/>
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190 <param argument="-evt" type="float" value="inf" label="E-value to stop looking for motifs"/>
0
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191 <conditional name="mod_type">
19
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192 <param name="mod_type_selector" argument="-mod" type="select" label="Expected motif distribution">
0
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193 <option value="oops">One Occurrence Per Sequence</option>
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194 <option value="zoops" selected="true">Zero or One Occurrence Per Sequence</option>
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195 <option value="anr">Any Number of Repetitions</option>
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196 </param>
19
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197 <when value="oops"/>
0
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198 <when value="zoops">
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199 <conditional name="motif_occurrence_type">
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200 <param name="motif_occurrence_type_selector" type="select" label="Number of motif occurrences">
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201 <option value="default" selected="true">Use defaults</option>
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202 <option value="nsites">nsites</option>
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203 <option value="min_max_sites">min and max sites</option>
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204 </param>
19
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205 <when value="default"/>
0
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206 <when value="nsites">
19
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207 <param argument="-nsites" type="integer" value="1" label="Search nsites number of occurrences"/>
0
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208 </when>
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209 <when value="min_max_sites">
19
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210 <param argument="-minsites" type="integer" value="1" label="minsites"/>
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211 <param argument="-maxsites" type="integer" value="50" label="maxsites"/>
0
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212 </when>
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213 </conditional>
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214 </when>
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215 <when value="anr">
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216 <conditional name="motif_occurrence_type">
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217 <param name="motif_occurrence_type_selector" type="select" label="Number of motif occurrences">
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218 <option value="default" selected="true">Use defaults</option>
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219 <option value="nsites">nsites</option>
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220 <option value="min_max_sites">min and max sites</option>
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221 </param>
19
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222 <when value="default"/>
0
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223 <when value="nsites">
19
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224 <param argument="-nsites" type="integer" value="1" label="Search nsites number of occurrences"/>
0
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225 </when>
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226 <when value="min_max_sites">
19
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227 <param argument="-minsites" type="integer" value="1" label="minsites"/>
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228 <param argument="-maxsites" type="integer" value="50" label="maxsites"/>
0
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229 </when>
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230 </conditional>
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231 </when>
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232 </conditional>
19
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233 <param argument="-wnsites" type="float" value="0.8" label="Weight on the prior on nsites"/>
0
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234 <conditional name="motif_width_type">
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235 <param name="motif_width_type_selector" type="select" label="Motif width type">
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236 <option value="exact">Exact width</option>
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237 <option value="range" selected="true">Specify a range</option>
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238 </param>
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239 <when value="exact">
19
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240 <param name="width" argument="-w" type="integer" value="10" label="Width of motif to search"/>
0
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241 </when>
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242 <when value="range">
19
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243 <param argument="-minw" type="integer" value="8" label="Min width of motif to search"/>
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244 <param argument="-maxw" type="integer" value="50" label="Max width of motif to search"/>
0
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245 </when>
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246 </conditional>
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247 <conditional name="motif_trim_type">
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248 <param name="motif_trim_type_selector" type="select" label="Motif trim type">
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249 <option value="nomatrim">No motif trim</option>
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250 <option value="trim" selected="true">Trim motif</option>
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251 </param>
19
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252 <when value="nomatrim"/>
0
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253 <when value="trim">
19
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254 <param argument="-wg" type="integer" value="11" label="Gap cost"/>
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255 <param argument="-ws" type="integer" value="1" label="Space cost"/>
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256 <param argument="-noendgaps" type="boolean" truevalue="-noendgaps" falsevalue="" checked="False" label="Do not penalize endgaps"/>
0
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257 </when>
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258 </conditional>
19
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259 <param argument="-bfile" type="data" format="txt" optional="True" label="Background Model"/>
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260 <param name="pspfile" argument="-psp" type="data" format="txt" optional="True" label="Position-Specific Prior"/>
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261 <param argument="-maxiter" type="integer" value="50" label="Number of iterations of EM to run"/>
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262 <param argument="-distance" type="float" value="0.001" label="Convergence criterion"/>
0
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263 <conditional name="branching_type">
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264 <param name="branching_type_selector" type="select" label="x-branching type">
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265 <option value="x_branch">Perform x-branching</option>
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266 <option value="no_x_branch" selected="true">No x-branching</option>
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267 </param>
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268 <when value="no_x_branch"/>
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269 <when value="x_branch">
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270 <param argument="-bfactor" type="integer" value="3" label="Number of iterations of branching"/>
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271 <param argument="-heapsize" type="integer" value="64" label="Maximum number of heaps to use"/>
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272 </when>
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273 </conditional>
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274 </when>
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275 </conditional>
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276 <param name="non_commercial_use" type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False" label="I certify that I am not using this tool for commercial purposes.">
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277 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
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278 </param>
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279 </inputs>
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280 <outputs>
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281 <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"/>
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282 <data format="txt" name="txt_outfile" label="${tool.name} on ${on_string} (text)"/>
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283 <data format="memexml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)"/>
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284 </outputs>
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285 <tests>
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286 <test>
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287 <param name="input1" value="meme_input_1.fasta" ftype="fasta" dbkey="hg19"/>
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288 <param name="options_type_selector" value="basic"/>
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289 <param name="non_commercial_use" value="True"/>
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290 <output name="html_outfile" file="meme_output_test1.html" compare="contains"/>
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291 <output name="txt_outfile" file="meme_output_test1.txt" compare="contains"/>
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292 <output name="xml_outfile" file="meme_output_test1.xml" compare="contains"/>
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293 </test>
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294 <test>
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295 <param name="input1" value="meme_input_1.fasta" ftype="fasta" dbkey="hg19"/>
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296 <param name="options_type_selector" value="advanced"/>
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297 <param name="plib" value="prior30.plib" ftype="txt"/>
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298 <param name="non_commercial_use" value="True"/>
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299 <output name="html_outfile" file="meme_output_test2.html" compare="contains"/>
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300 <output name="txt_outfile" file="meme_output_test2.txt" compare="contains"/>
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301 <output name="xml_outfile" file="meme_output_test2.xml" compare="contains"/>
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302 </test>
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303 </tests>
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304 <help>
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305
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306 .. class:: warningmark
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307
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308 **WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted.
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309 Before using, be sure to review, agree, and comply with the license.**
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310
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311 If you want to specify sequence weights, you must include them at the top of your input FASTA file.
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312
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313 MEME discovers novel, ungapped motifs (recurring, fixed-length patterns) in your sequences (sample output from sequences).
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314 MEME splits variable-length patterns into two or more separate motifs. A motif is a sequence pattern that occurs repeatedly
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315 in a group of related sequences. MEME represents motifs as position-dependent letter-probability matrices which describe the
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316 probability of each possible letter at each position in the pattern. Individual MEME motifs do not contain gaps. Patterns
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317 with variable-length gaps are split by MEME into two or more separate motifs. MEME takes as input a group of sequences and
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318 outputs as many motifs as requested. MEME uses statistical modeling techniques to automatically choose the best width, number
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319 of occurrences, and description for each motif.
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320
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321 .. class:: infomark
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322
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323 For detailed information on MEME, click here_, or view the license_.
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324
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325 .. _here: http://meme-suite.org/doc/meme.html?man_type=web
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326 .. _license: http://meme-suite.org/doc/copyright.html?man_type=web
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327
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328 </help>
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329 <citations>
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330 <citation type="bibtex">
11
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331 @inproceedings{Bailey1994Fitting,
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332 booktitle = {Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology},
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333 pages = {28-36},
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334 author = {Bailey, Timothy L. and Elkan, Charles},
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335 title = {Fitting a mixture model by expectation maximization to discover motifs in biopolymers},
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336 url = {https://www.aaai.org/Papers/ISMB/1994/ISMB94-004.pdf},
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337 year = {1994}
11
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338 }
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339 </citation>
0
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340 </citations>
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341 </tool>