Mercurial > repos > iuc > meme_meme
annotate meme.xml @ 16:3c2ac7c3f0b8 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 8c1eac566cbcc93ceb3d753170bce144d386722c"
author | iuc |
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date | Sat, 27 Nov 2021 09:45:12 +0000 |
parents | 9dd5373f6a5a |
children | 19237efe98d1 |
rev | line source |
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16
3c2ac7c3f0b8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 8c1eac566cbcc93ceb3d753170bce144d386722c"
iuc
parents:
15
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changeset
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1 <tool id="meme_meme" name="MEME" version="@TOOL_VERSION@.0"> |
13
57e5d9382f36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
iuc
parents:
11
diff
changeset
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2 <description>- Multiple EM for Motif Elicitation</description> |
16
3c2ac7c3f0b8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 8c1eac566cbcc93ceb3d753170bce144d386722c"
iuc
parents:
15
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3 <xrefs> |
3c2ac7c3f0b8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 8c1eac566cbcc93ceb3d753170bce144d386722c"
iuc
parents:
15
diff
changeset
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4 <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
diff
changeset
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5 </xrefs> |
9
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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6 <macros> |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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7 <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
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8 </macros> |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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9 <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
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10 <command detect_errors="exit_code"><![CDATA[ |
16
3c2ac7c3f0b8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 8c1eac566cbcc93ceb3d753170bce144d386722c"
iuc
parents:
15
diff
changeset
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11 @CHECK_NON_COMMERCIAL_USE@ |
15
9dd5373f6a5a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
iuc
parents:
14
diff
changeset
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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:
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changeset
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13 |
9
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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14 meme '$input1' |
15
9dd5373f6a5a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
iuc
parents:
14
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changeset
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15 -p \${GALAXY_SLOTS:-1} |
9
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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16 -o '${html_outfile.files_path}' |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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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
diff
changeset
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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
diff
changeset
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19 #if str( $options_type.options_type_selector ) == 'advanced': |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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20 -sf '${ str( $options_type.sf ).replace( " ", "_" ) }' |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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21 -${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
diff
changeset
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22 -mod '${options_type.mod_type.mod_type_selector}' |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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23 -nmotifs '${options_type.nmotifs}' |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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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
diff
changeset
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25 #if $options_type.evt < float('inf'): |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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26 -evt '${options_type.evt}' |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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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
diff
changeset
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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
diff
changeset
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29 #if str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'nsites': |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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30 -nsites '${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
diff
changeset
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31 #elif str( $options_type.mod_type.motif_occurrence_type.motif_occurrence_type_selector ) == 'min_max_sites': |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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32 -minsites '${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
diff
changeset
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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
parents:
7
diff
changeset
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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
diff
changeset
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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
diff
changeset
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36 #if str( $options_type.motif_width_type.motif_width_type_selector ) == 'exact': |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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37 -w '${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
diff
changeset
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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
diff
changeset
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39 -minw '${options_type.motif_width_type.minw}' |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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40 -maxw '${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
diff
changeset
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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
diff
changeset
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42 #if str( $options_type.motif_trim_type.motif_trim_type_selector ) == 'nomatrim': |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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43 -nomatrim |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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44 #else |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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45 -wg '${options_type.motif_trim_type.wg}' |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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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
iuc
parents:
7
diff
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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
iuc
parents:
7
diff
changeset
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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
parents:
7
diff
changeset
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49 #if str( $options_type.bfile ) != 'None': |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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50 -bfile '${options_type.bfile}' |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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51 #end if |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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52 #if str( $options_type.pspfile ) != 'None': |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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53 -psp '${options_type.pspfile}' |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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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
parents:
7
diff
changeset
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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
iuc
parents:
7
diff
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56 ${options_type.alphabet_type.revcomp} ${options_type.alphabet_type.pal} |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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57 #end if |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
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58 -maxiter '${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
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59 -distance '${options_type.distance}' |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
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60 -prior '${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
iuc
parents:
7
diff
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61 #if str( $options_type.alphabet_type.prior_type.prior_type_selector ) != 'addone': |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
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62 -b '${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
parents:
7
diff
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63 #if str( $options_type.alphabet_type.prior_type.plib ) != 'None': |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
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64 -plib '${options_type.alphabet_type.prior_type.plib}' |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
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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
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66 #end if |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
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67 #if str( $options_type.alphabet_type.spmap_type.spmap_type_selector ) == 'cons': |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
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68 -cons '${options_type.alphabet_type.spmap_type.cons}' |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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69 #else |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
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70 -spmap '${options_type.alphabet_type.spmap_type.spmap_type_selector}' |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
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71 -spfuzz '${options_type.alphabet_type.spmap_type.spfuzz}' |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
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72 #end if |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
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73 #if str( $options_type.branching_type.branching_type_selector ) == 'x_branch': |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
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diff
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74 -x_branch |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
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75 -bfactor '${options_type.branching_type.bfactor}' |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
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76 -heapsize '${options_type.branching_type.heapsize}' |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
7
diff
changeset
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77 #end if |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
iuc
parents:
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|
78 #end if |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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79 && mv '${html_outfile.files_path}/meme.html' '${html_outfile}' |
794b2859c286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 211bfa0f58a0691fb7b0c2623763112fdcb76dbd
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diff
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80 && mv '${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
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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|
83 <inputs> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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84 <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
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changeset
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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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|
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
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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
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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
iuc
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changeset
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89 </param> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
iuc
parents:
diff
changeset
|
90 <when value="basic" /> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
iuc
parents:
diff
changeset
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91 <when value="advanced"> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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92 <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
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changeset
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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
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changeset
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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
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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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changeset
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97 </param> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
iuc
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98 <when value="protein"> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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99 <conditional name="prior_type"> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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100 <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
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changeset
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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
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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
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changeset
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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
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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> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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107 <when value="dirichlet"> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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108 <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
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109 <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
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110 </when> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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111 <when value="dmix"> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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112 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/> |
e416c7c26977
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113 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/> |
e416c7c26977
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114 </when> |
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115 <when value="mega"> |
e416c7c26977
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116 <param name="prior_b" type="float" value="0" label="strength of prior on model parameters" argument="-b"/> |
e416c7c26977
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117 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/> |
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118 </when> |
e416c7c26977
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119 <when value="megap"> |
e416c7c26977
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120 <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
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121 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/> |
e416c7c26977
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122 </when> |
e416c7c26977
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123 <when value="addone" /> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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124 </conditional> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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125 <conditional name="spmap_type"> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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126 <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
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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
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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
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129 <option value="cons">Use starting point from string</option> |
e416c7c26977
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130 </param> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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131 <when value="uni"> |
e416c7c26977
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132 <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
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133 </when> |
e416c7c26977
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134 <when value="pam"> |
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135 <param name="spfuzz" type="integer" value="120" label="Fuzziness of the mapping" argument="-spfuzz"/> |
e416c7c26977
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136 </when> |
e416c7c26977
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137 <when value="cons"> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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138 <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
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139 </when> |
e416c7c26977
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140 </conditional> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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141 </when> |
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142 <when value="dna"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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143 <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
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144 <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
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145 <conditional name="prior_type"> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
iuc
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146 <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
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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
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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
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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
iuc
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152 </param> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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153 <when value="dirichlet"> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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154 <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
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155 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/> |
e416c7c26977
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156 </when> |
e416c7c26977
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iuc
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157 <when value="dmix"> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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158 <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
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159 <param name="plib" type="data" format="txt" optional="True" label="Dirichlet prior file" argument="-plib"/> |
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160 </when> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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changeset
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161 <when value="mega"> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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162 <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
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163 <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
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changeset
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164 </when> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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165 <when value="megap"> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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166 <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
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167 <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
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168 </when> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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169 <when value="addone" /> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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170 </conditional> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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171 <conditional name="spmap_type"> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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172 <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
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173 <option value="uni" selected="true">uni</option> |
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174 <option value="pam">pam</option> |
e416c7c26977
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175 <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
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176 </param> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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177 <when value="uni"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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178 <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
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179 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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180 <when value="pam"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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181 <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
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182 </when> |
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183 <when value="cons"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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184 <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
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185 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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186 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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187 </when> |
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188 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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189 <param name="nmotifs" type="integer" value="1" label="Number of different motifs to search" argument="-nmotifs" /> |
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190 <param name="evt" type="float" value="inf" label="E-value to stop looking for motifs" argument="-evt"/> |
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191 <conditional name="mod_type"> |
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192 <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
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193 <option value="oops">One Occurrence Per Sequence</option> |
e416c7c26977
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194 <option value="zoops" selected="true">Zero or One Occurrence Per Sequence</option> |
e416c7c26977
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195 <option value="anr">Any Number of Repetitions</option> |
e416c7c26977
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196 </param> |
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iuc
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197 <when value="oops" /> |
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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"> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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201 <option value="default" selected="true">Use defaults</option> |
e416c7c26977
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202 <option value="nsites">nsites</option> |
e416c7c26977
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203 <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
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204 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
iuc
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205 <when value="default" /> |
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206 <when value="nsites"> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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207 <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
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208 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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209 <when value="min_max_sites"> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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210 <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
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211 <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
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212 </when> |
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213 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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214 </when> |
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215 <when value="anr"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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216 <conditional name="motif_occurrence_type"> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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217 <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
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218 <option value="default" selected="true">Use defaults</option> |
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219 <option value="nsites">nsites</option> |
e416c7c26977
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220 <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
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221 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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222 <when value="default" /> |
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223 <when value="nsites"> |
e416c7c26977
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224 <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
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225 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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226 <when value="min_max_sites"> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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227 <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
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228 <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
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229 </when> |
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230 </conditional> |
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231 </when> |
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232 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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233 <param name="wnsites" type="float" value="0.8" label="Weight on the prior on nsites" argument="-wnsites"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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234 <conditional name="motif_width_type"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
iuc
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235 <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
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236 <option value="exact">Exact width</option> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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237 <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
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238 </param> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
iuc
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239 <when value="exact"> |
e416c7c26977
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
iuc
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240 <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
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241 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
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242 <when value="range"> |
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243 <param name="minw" type="integer" value="8" label="Min width of motif to search" argument="-minw"/> |
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244 <param name="maxw" type="integer" value="50" label="Max width of motif to search" argument="-maxw"/> |
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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> |
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252 <when value="nomatrim" /> |
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253 <when value="trim"> |
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254 <param name="wg" type="integer" value="11" label="Gap cost" argument="-wg"/> |
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255 <param name="ws" type="integer" value="1" label="Space cost" argument="-ws"/> |
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256 <param name="noendgaps" label="Do not penalize endgaps" type="boolean" truevalue="-noendgaps" falsevalue="" checked="False"/> |
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257 </when> |
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258 </conditional> |
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259 <param name="bfile" type="data" format="txt" optional="True" label="Background Model" argument="-bfile"/> |
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260 <param name="pspfile" type="data" format="txt" optional="True" label="Position-Specific Prior" argument="-psp"/> |
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261 <param name="maxiter" type="integer" value="50" label="Number of iterations of EM to run" argument="-maxiter"/> |
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262 <param name="distance" type="float" value="0.001" label="Convergence criterion" argument="-distance"/> |
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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 name="bfactor" type="integer" value="3" label="Number of iterations of branching" argument="-bfactor"/> |
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271 <param name="heapsize" type="integer" value="64" label="Maximum number of heaps to use" argument="-heapsize"/> |
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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" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False"> |
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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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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
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300 <output name="txt_outfile" file="meme_output_test2.txt" compare="contains"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
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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"> |
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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} |
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338 } |
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339 </citation> |
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340 </citations> |
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341 </tool> |