meme_chip: meme_chip.xml annotate

annotate meme_chip.xml @ 9:4fc125833bc2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3

author	iuc
date	Thu, 15 Nov 2018 09:57:52 -0500
parents	81c0806236ef
children	c0b3721b69a7

rev	line source
9 4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	1 <tool id="meme_chip" name="MEME-ChIP" version="@WRAPPER_VERSION@+galaxy1">
0 fd58302909b8 Uploaded iuc parents: diff changeset	2 <description>- motif discovery, enrichment analysis and clustering on large nucleotide datasets</description>
fd58302909b8 Uploaded iuc parents: diff changeset	3 <macros>
fd58302909b8 Uploaded iuc parents: diff changeset	4 <import>macros.xml</import>
fd58302909b8 Uploaded iuc parents: diff changeset	5 </macros>
fd58302909b8 Uploaded iuc parents: diff changeset	6 <expand macro="requirements" />
5 ff7dc6057652 Uploaded iuc parents: 3 diff changeset	7 <code file="get_meme_motif_databases.py" />
0 fd58302909b8 Uploaded iuc parents: diff changeset	8 <command detect_errors="exit_code"><![CDATA[
3 8d3877046d78 Uploaded iuc parents: 0 diff changeset	9 #import os
8d3877046d78 Uploaded iuc parents: 0 diff changeset	10 #set primary_output = $os.path.join($output.files_path, "index.html")
5 ff7dc6057652 Uploaded iuc parents: 3 diff changeset	11 meme-chip '$input'
0 fd58302909b8 Uploaded iuc parents: diff changeset	12 -noecho
6 444093446b0b Uploaded iuc parents: 5 diff changeset	13 #if $control:
3 8d3877046d78 Uploaded iuc parents: 0 diff changeset	14 -neg '$control'
8d3877046d78 Uploaded iuc parents: 0 diff changeset	15 #end if
6 444093446b0b Uploaded iuc parents: 5 diff changeset	16 $sequence_alphabet
0 fd58302909b8 Uploaded iuc parents: diff changeset	17 -o '$output.files_path'
7 c321ab02c2a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742 iuc parents: 6 diff changeset	18 #if str($options_type_cond.options_type)=='advanced':
9 4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	19 ## FIXME: CentriMo cannot be run, See the comments in the input section.
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	20 ## #set run_centrimo = $options_type_cond.run_centrimo_cond.run_centrimo
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	21 ## #if str($run_centrimo) == "yes":
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	22 ## -db $options_type_cond.run_centrimo_cond.meme_motif_databases.fields.path
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	23 ## #if $options_type_cond.run_centrimo_cond.centrimo_local:
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	24 ## -centrimo-local
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	25 ## #end if
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	26 ## #if $options_type_cond.run_centrimo_cond.centrimo_score:
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	27 ## -centrimo-score $options_type_cond.run_centrimo_cond.centrimo_score
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	28 ## #end if
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	29 ## #if $options_type_cond.run_centrimo_cond.centrimo_maxreg:
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	30 ## -centrimo-maxreg $options_type_cond.run_centrimo_cond.centrimo_maxreg
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	31 ## #end if
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	32 ## #if $options_type_cond.run_centrimo_cond.centrimo_ethresh:
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	33 ## -centrimo-ethresh $options_type_cond.run_centrimo_cond.centrimo_ethresh
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	34 ## #end if
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	35 ## #if $options_type_cond.run_centrimo_cond.centrimo_noseq:
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	36 ## -centrimo-noseq
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	37 ## #end if
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	38 ## #if $options_type_cond.run_centrimo_cond.centrimo_flip:
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	39 ## -centrimo-flip
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	40 ## #end if
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	41 ## #end if
7 c321ab02c2a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742 iuc parents: 6 diff changeset	42 $options_type_cond.search_given_strand
0 fd58302909b8 Uploaded iuc parents: diff changeset	43 -order $options_type_cond.background_model_order
3 8d3877046d78 Uploaded iuc parents: 0 diff changeset	44 #if str($options_type_cond.subsampling_cond.subsampling) == "no":
0 fd58302909b8 Uploaded iuc parents: diff changeset	45 -norand
7 c321ab02c2a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742 iuc parents: 6 diff changeset	46 #if $options_type_cond.subsampling_cond.subsampling.seed:
0 fd58302909b8 Uploaded iuc parents: diff changeset	47 -seed $options_type_cond.subsampling_cond.subsampling.seed
fd58302909b8 Uploaded iuc parents: diff changeset	48 #end if
fd58302909b8 Uploaded iuc parents: diff changeset	49 #end if
6 444093446b0b Uploaded iuc parents: 5 diff changeset	50 #if $options_type_cond.nmeme:
0 fd58302909b8 Uploaded iuc parents: diff changeset	51 -nmeme $options_type_cond.nmeme
fd58302909b8 Uploaded iuc parents: diff changeset	52 #end if
6 444093446b0b Uploaded iuc parents: 5 diff changeset	53 #if $options_type_cond.ccut:
0 fd58302909b8 Uploaded iuc parents: diff changeset	54 -ccut $options_type_cond.ccut
fd58302909b8 Uploaded iuc parents: diff changeset	55 #end if
fd58302909b8 Uploaded iuc parents: diff changeset	56 -group-thresh $options_type_cond.group_threash
7 c321ab02c2a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742 iuc parents: 6 diff changeset	57 #if str($options_type_cond.group_weak):
0 fd58302909b8 Uploaded iuc parents: diff changeset	58 -group-weak $options_type_cond.group_weak
fd58302909b8 Uploaded iuc parents: diff changeset	59 #end if
5 ff7dc6057652 Uploaded iuc parents: 3 diff changeset	60 -filter-thresh $options_type_cond.filter_thresh
7 c321ab02c2a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742 iuc parents: 6 diff changeset	61 $options_type_cond.old_clustering
0 fd58302909b8 Uploaded iuc parents: diff changeset	62 -meme-mod $options_type_cond.meme_mod
6 444093446b0b Uploaded iuc parents: 5 diff changeset	63 #if $options_type_cond.meme_minw:
0 fd58302909b8 Uploaded iuc parents: diff changeset	64 -meme-minw $options_type_cond.meme_minw
fd58302909b8 Uploaded iuc parents: diff changeset	65 #end if
6 444093446b0b Uploaded iuc parents: 5 diff changeset	66 #if $options_type_cond.meme_maxw:
0 fd58302909b8 Uploaded iuc parents: diff changeset	67 -meme-maxw $options_type_cond.meme_maxw
fd58302909b8 Uploaded iuc parents: diff changeset	68 #end if
6 444093446b0b Uploaded iuc parents: 5 diff changeset	69 #if $options_type_cond.meme_nmotifs:
0 fd58302909b8 Uploaded iuc parents: diff changeset	70 -meme-nmotifs $options_type_cond.meme_nmotifs
fd58302909b8 Uploaded iuc parents: diff changeset	71 #end if
6 444093446b0b Uploaded iuc parents: 5 diff changeset	72 #if $options_type_cond.meme_minsites:
0 fd58302909b8 Uploaded iuc parents: diff changeset	73 -meme-minsites $options_type_cond.meme_minsites
fd58302909b8 Uploaded iuc parents: diff changeset	74 #end if
6 444093446b0b Uploaded iuc parents: 5 diff changeset	75 #if $options_type_cond.meme_maxsites:
0 fd58302909b8 Uploaded iuc parents: diff changeset	76 -meme-maxsites $options_type_cond.meme_maxsites
fd58302909b8 Uploaded iuc parents: diff changeset	77 #end if
7 c321ab02c2a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742 iuc parents: 6 diff changeset	78 $options_type_cond.meme_pal
0 fd58302909b8 Uploaded iuc parents: diff changeset	79 -dreme-e $options_type_cond.dreme_e
fd58302909b8 Uploaded iuc parents: diff changeset	80 -dreme-m $options_type_cond.dreme_m
fd58302909b8 Uploaded iuc parents: diff changeset	81 -spamo-skip
fd58302909b8 Uploaded iuc parents: diff changeset	82 -fimo-skip
fd58302909b8 Uploaded iuc parents: diff changeset	83 #end if
9 4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	84 && mv $primary_output '$output'
3 8d3877046d78 Uploaded iuc parents: 0 diff changeset	85 ]]></command>
0 fd58302909b8 Uploaded iuc parents: diff changeset	86 <inputs>
fd58302909b8 Uploaded iuc parents: diff changeset	87 <param name="input" type="data" format="fasta" label="Primary sequences" help="Nucleotide sequences must have equal length"/>
3 8d3877046d78 Uploaded iuc parents: 0 diff changeset	88 <param name="control" type="data" format="fasta" optional="true" label="Control sequences" help="If no selection, positive sequences in the input are shuffled to create the negative set"/>
0 fd58302909b8 Uploaded iuc parents: diff changeset	89 <param name="sequence_alphabet" type="select" label="Sequence alphabet">
5 ff7dc6057652 Uploaded iuc parents: 3 diff changeset	90 <option value="-dna" selected="true">DNA</option>
ff7dc6057652 Uploaded iuc parents: 3 diff changeset	91 <option value="-rna">RNA</option>
0 fd58302909b8 Uploaded iuc parents: diff changeset	92 </param>
fd58302909b8 Uploaded iuc parents: diff changeset	93 <conditional name="options_type_cond">
fd58302909b8 Uploaded iuc parents: diff changeset	94 <param name="options_type" type="select" label="Options Configuration">
fd58302909b8 Uploaded iuc parents: diff changeset	95 <option value="basic" selected="true">Basic</option>
fd58302909b8 Uploaded iuc parents: diff changeset	96 <option value="advanced">Advanced</option>
fd58302909b8 Uploaded iuc parents: diff changeset	97 </param>
fd58302909b8 Uploaded iuc parents: diff changeset	98 <when value="basic"/>
fd58302909b8 Uploaded iuc parents: diff changeset	99 <when value="advanced">
9 4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	100 <!--
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	101 FIXME: CentriMo cannot be run since the tool form cannot populate the mem_motif_database select list below.
3 8d3877046d78 Uploaded iuc parents: 0 diff changeset	102 <conditional name="run_centrimo_cond">
8d3877046d78 Uploaded iuc parents: 0 diff changeset	103 <param name="run_centrimo" type="select" label="Run TOMTOM and CentriMo?">
8d3877046d78 Uploaded iuc parents: 0 diff changeset	104 <option value="yes" selected="true">Yes</option>
8d3877046d78 Uploaded iuc parents: 0 diff changeset	105 <option value="no">No</option>
8d3877046d78 Uploaded iuc parents: 0 diff changeset	106 </param>
8d3877046d78 Uploaded iuc parents: 0 diff changeset	107 <when value="yes">
9 4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	108
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	109 We have 2 dynamic select lists here. The first select list (meme_motif_database_dir) is populated from the meme_motif_databases
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	110 data table. The second select list (meme_motif_database) is dynamically re-rendered whenever the selection in the meme_motif_database_dir
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	111 select list is changed. This composition used to work (see Examples->Dynamic Options section of
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	112 https://docs.galaxyproject.org/en/latest/dev/schema.html) but no longer does. We'll have to figure out what is broken in
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	113 the dynamic options code in ~/parameters/basic.py in order to uncomment this block.
4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	114
3 8d3877046d78 Uploaded iuc parents: 0 diff changeset	115 <param name="meme_motif_database_dir" type="select" label="Select the motifs (DNA)" refresh_on_change="True">
8d3877046d78 Uploaded iuc parents: 0 diff changeset	116 <options from_data_table="meme_motif_databases">
8d3877046d78 Uploaded iuc parents: 0 diff changeset	117 <filter type="sort_by" column="1"/>
8d3877046d78 Uploaded iuc parents: 0 diff changeset	118 <validator type="no_options" message="No MEME motif databases are available for the selected input"/>
8d3877046d78 Uploaded iuc parents: 0 diff changeset	119 </options>
8d3877046d78 Uploaded iuc parents: 0 diff changeset	120 </param>
8d3877046d78 Uploaded iuc parents: 0 diff changeset	121 <param name="meme_motif_database" type="select" label="MEME motif database" dynamic_options="get_meme_motif_database_options(file_path=meme_motif_database_dir)"/>
8d3877046d78 Uploaded iuc parents: 0 diff changeset	122 <param name="centrimo_local" type="boolean" truevalue="true" falsevalue="" checked="False" label="Compute enrichment of all regions"/>
5 ff7dc6057652 Uploaded iuc parents: 3 diff changeset	123 <param name="centrimo_score" type="integer" optional="true" value="0" min="0" label="Minimum allowed CentriMo match score"/>
ff7dc6057652 Uploaded iuc parents: 3 diff changeset	124 <param name="centrimo_maxreg" type="integer" optional="true" value="0" min="0" label="Maximum CentriMo region size to be considered"/>
ff7dc6057652 Uploaded iuc parents: 3 diff changeset	125 <param name="centrimo_ethresh" type="integer" optional="true" value="0" min="0" label="CentriMo E-value threshold for reporting" />
3 8d3877046d78 Uploaded iuc parents: 0 diff changeset	126 <param name="centrimo_noseq" type="boolean" truevalue="true" falsevalue="" checked="False" label="Store CentriMo sequence IDs in the output"/>
8d3877046d78 Uploaded iuc parents: 0 diff changeset	127 <param name="centrimo_flip" type="boolean" truevalue="true" falsevalue="" checked="False" label="Reflect CentriMo matches on reverse strand around center"/>
8d3877046d78 Uploaded iuc parents: 0 diff changeset	128 </when>
8d3877046d78 Uploaded iuc parents: 0 diff changeset	129 <when value="no"/>
8d3877046d78 Uploaded iuc parents: 0 diff changeset	130 </conditional>
9 4fc125833bc2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 0ba5f658424430eea10c79f92c9a8d7a1ca9eaf3 iuc parents: 8 diff changeset	131 -->
0 fd58302909b8 Uploaded iuc parents: diff changeset	132 <param name="background_model_order" type="select" label="Select the order of the Markov background model">
fd58302909b8 Uploaded iuc parents: diff changeset	133 <option value="0">0-order model of sequences</option>
fd58302909b8 Uploaded iuc parents: diff changeset	134 <option value="1" selected="True">1st order model of sequences</option>
fd58302909b8 Uploaded iuc parents: diff changeset	135 <option value="2">2nd order model of sequences</option>
fd58302909b8 Uploaded iuc parents: diff changeset	136 <option value="3">3rd order model of sequences</option>
fd58302909b8 Uploaded iuc parents: diff changeset	137 <option value="4">4th order model of sequences</option>
fd58302909b8 Uploaded iuc parents: diff changeset	138 </param>
7 c321ab02c2a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742 iuc parents: 6 diff changeset	139 <param name="nmeme" type="integer" optional="true" value="" min="1" label="Limit of sequences to pass to MEME"/>
0 fd58302909b8 Uploaded iuc parents: diff changeset	140 <conditional name="subsampling_cond">
fd58302909b8 Uploaded iuc parents: diff changeset	141 <param name="subsampling" type="select" label="Should subsampling be random?" help="Select 'No' if your input sequences are sorted in order of confidence (best to worst)">
fd58302909b8 Uploaded iuc parents: diff changeset	142 <option value="yes" selected="true">Yes</option>
fd58302909b8 Uploaded iuc parents: diff changeset	143 <option value="no">No</option>
fd58302909b8 Uploaded iuc parents: diff changeset	144 </param>
fd58302909b8 Uploaded iuc parents: diff changeset	145 <when value="yes">
7 c321ab02c2a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742 iuc parents: 6 diff changeset	146 <param name="seed" type="integer" optional="true" value="" min="1" label="Seed for the randomized selection of sequences"/>
0 fd58302909b8 Uploaded iuc parents: diff changeset	147 </when>
fd58302909b8 Uploaded iuc parents: diff changeset	148 <when value="no"/>
fd58302909b8 Uploaded iuc parents: diff changeset	149 </conditional>
5 ff7dc6057652 Uploaded iuc parents: 3 diff changeset	150 <param name="ccut" type="integer" optional="true" value="100" min="0" label="maximum size of a sequence before it is cut down to a centered section" help="Zero value indicates the sequences should not be cut down"/>
0 fd58302909b8 Uploaded iuc parents: diff changeset	151 <param name="group_threash" type="float" value="0.05" min="0" label="Primary threshold for clustering motifs" />
5 ff7dc6057652 Uploaded iuc parents: 3 diff changeset	152 <param name="group_weak" type="float" optional="true" value="0" min="0" label="Secondary threshold for clustering motifs" help="Zero value results in 2*primary threshold"/>
0 fd58302909b8 Uploaded iuc parents: diff changeset	153 <param name="filter_thresh" type="float" value="0.05" min="0" label="E-value threshold for including motifs"/>
7 c321ab02c2a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742 iuc parents: 6 diff changeset	154 <param name="search_given_strand" type="boolean" truevalue="-norc" falsevalue="" checked="False" label="Search given strand only"/>
c321ab02c2a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742 iuc parents: 6 diff changeset	155 <param argument="-old_clustering" type="boolean" truevalue="-old_clustering" falsevalue="" checked="False" label="Pick cluster seed motifs based only on significance"/>
0 fd58302909b8 Uploaded iuc parents: diff changeset	156 <param name="meme_mod" type="select" label="What is the expected motif site distribution?">
fd58302909b8 Uploaded iuc parents: diff changeset	157 <option value="oops" selected="True">One occurance per sequence</option>
fd58302909b8 Uploaded iuc parents: diff changeset	158 <option value="zoops">Zero or one occurances per sequence</option>
fd58302909b8 Uploaded iuc parents: diff changeset	159 <option value="anr">Any number of repititions</option>
fd58302909b8 Uploaded iuc parents: diff changeset	160 </param>
5 ff7dc6057652 Uploaded iuc parents: 3 diff changeset	161 <param name="meme_minw" type="integer" optional="true" value="0" min="0" label="Minimum motif width"/>
ff7dc6057652 Uploaded iuc parents: 3 diff changeset	162 <param name="meme_maxw" type="integer" optional="true" value="0" min="0" label="Maximum motif width"/>
ff7dc6057652 Uploaded iuc parents: 3 diff changeset	163 <param name="meme_nmotifs" type="integer" optional="true" value="0" min="0" label="Maximum number of motifs to find"/>
ff7dc6057652 Uploaded iuc parents: 3 diff changeset	164 <param name="meme_minsites" type="integer" optional="true" value="0" min="0" label="Minimum number of sites per motif"/>
ff7dc6057652 Uploaded iuc parents: 3 diff changeset	165 <param name="meme_maxsites" type="integer" optional="true" value="0" label="Maximum number of sites per motif"/>
7 c321ab02c2a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme_chip commit 9068afc3812495aaf88c9a2f5a224c634d634742 iuc parents: 6 diff changeset	166 <param argument="-meme_pal" type="boolean" truevalue="-meme-pal" falsevalue="" checked="False" label="Look for palindromes only"/>
0 fd58302909b8 Uploaded iuc parents: diff changeset	167 <param name="dreme_e" type="float" value="0.05" min="0" label="Stop DREME searching after reaching this E-value threshold"/>
fd58302909b8 Uploaded iuc parents: diff changeset	168 <param name="dreme_m" type="integer" value="10" min="1" label="Stop DREME searching after finding this many motifs" />
fd58302909b8 Uploaded iuc parents: diff changeset	169 </when>
fd58302909b8 Uploaded iuc parents: diff changeset	170 </conditional>
fd58302909b8 Uploaded iuc parents: diff changeset	171 <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">
fd58302909b8 Uploaded iuc parents: diff changeset	172 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
fd58302909b8 Uploaded iuc parents: diff changeset	173 </param>
fd58302909b8 Uploaded iuc parents: diff changeset	174 </inputs>
fd58302909b8 Uploaded iuc parents: diff changeset	175 <outputs>
fd58302909b8 Uploaded iuc parents: diff changeset	176 <data name="output" format="html" label="${tool.name} (html) on ${on_string}"/>
fd58302909b8 Uploaded iuc parents: diff changeset	177 </outputs>
fd58302909b8 Uploaded iuc parents: diff changeset	178 <tests>
fd58302909b8 Uploaded iuc parents: diff changeset	179 <test>
5 ff7dc6057652 Uploaded iuc parents: 3 diff changeset	180 <param name="input" value="input1.fasta" ftype="fasta"/>
ff7dc6057652 Uploaded iuc parents: 3 diff changeset	181 <param name="non_commercial_use" value="True"/>
ff7dc6057652 Uploaded iuc parents: 3 diff changeset	182 <output name="output" file="output1.html" ftype="html" compare="contains"/>
ff7dc6057652 Uploaded iuc parents: 3 diff changeset	183 </test>
ff7dc6057652 Uploaded iuc parents: 3 diff changeset	184 <test>
ff7dc6057652 Uploaded iuc parents: 3 diff changeset	185 <param name="input" value="input1.fasta" ftype="fasta"/>
6 444093446b0b Uploaded iuc parents: 5 diff changeset	186 <param name="sequence_alphabet" value="-rna"/>
5 ff7dc6057652 Uploaded iuc parents: 3 diff changeset	187 <param name="options_type" value="advanced"/>
ff7dc6057652 Uploaded iuc parents: 3 diff changeset	188 <param name="background_model_order" value="0"/>
ff7dc6057652 Uploaded iuc parents: 3 diff changeset	189 <param name="non_commercial_use" value="True"/>
ff7dc6057652 Uploaded iuc parents: 3 diff changeset	190 <output name="output" file="output1.html" ftype="html" compare="contains"/>
0 fd58302909b8 Uploaded iuc parents: diff changeset	191 </test>
fd58302909b8 Uploaded iuc parents: diff changeset	192 </tests>
fd58302909b8 Uploaded iuc parents: diff changeset	193 <help>
fd58302909b8 Uploaded iuc parents: diff changeset	194 .. class:: warningmark
fd58302909b8 Uploaded iuc parents: diff changeset	195
fd58302909b8 Uploaded iuc parents: diff changeset	196 **WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted.
fd58302909b8 Uploaded iuc parents: diff changeset	197 Before using, be sure to review, agree, and comply with the license.**
fd58302909b8 Uploaded iuc parents: diff changeset	198
fd58302909b8 Uploaded iuc parents: diff changeset	199 MWMW-ChIP perform motif discovery, motif enrichment analysis and clustering on large nucleotide datasets.
fd58302909b8 Uploaded iuc parents: diff changeset	200
fd58302909b8 Uploaded iuc parents: diff changeset	201 If you want to specify sequence weights, you must include them at the top of your input FASTA file.
fd58302909b8 Uploaded iuc parents: diff changeset	202
fd58302909b8 Uploaded iuc parents: diff changeset	203 MEME discovers novel, ungapped motifs (recurring, fixed-length patterns) in your sequences (sample output from sequences).
fd58302909b8 Uploaded iuc parents: diff changeset	204 MEME splits variable-length patterns into two or more separate motifs. A motif is a sequence pattern that occurs repeatedly
fd58302909b8 Uploaded iuc parents: diff changeset	205 in a group of related sequences. MEME represents motifs as position-dependent letter-probability matrices which describe the
fd58302909b8 Uploaded iuc parents: diff changeset	206 probability of each possible letter at each position in the pattern. Individual MEME motifs do not contain gaps. Patterns
fd58302909b8 Uploaded iuc parents: diff changeset	207 with variable-length gaps are split by MEME into two or more separate motifs. MEME takes as input a group of sequences and
fd58302909b8 Uploaded iuc parents: diff changeset	208 outputs as many motifs as requested. MEME uses statistical modeling techniques to automatically choose the best width, number
fd58302909b8 Uploaded iuc parents: diff changeset	209 of occurrences, and description for each motif.
fd58302909b8 Uploaded iuc parents: diff changeset	210
fd58302909b8 Uploaded iuc parents: diff changeset	211 .. class:: infomark
fd58302909b8 Uploaded iuc parents: diff changeset	212
fd58302909b8 Uploaded iuc parents: diff changeset	213 For detailed information on MEME, click here_, or view the license_.
fd58302909b8 Uploaded iuc parents: diff changeset	214
fd58302909b8 Uploaded iuc parents: diff changeset	215 .. _here: http://meme-suite.org/doc/meme.html?man_type=web
fd58302909b8 Uploaded iuc parents: diff changeset	216 .. _license: http://meme-suite.org/doc/copyright.html?man_type=web
fd58302909b8 Uploaded iuc parents: diff changeset	217
fd58302909b8 Uploaded iuc parents: diff changeset	218 </help>
fd58302909b8 Uploaded iuc parents: diff changeset	219 <citations>
3 8d3877046d78 Uploaded iuc parents: 0 diff changeset	220 <citation type="doi">10.1093/bioinformatics/btr189</citation>
0 fd58302909b8 Uploaded iuc parents: diff changeset	221 </citations>
fd58302909b8 Uploaded iuc parents: diff changeset	222 </tool>
3 8d3877046d78 Uploaded iuc parents: 0 diff changeset	223

Mercurial > repos > iuc > meme_chip

annotate meme_chip.xml @ 9:4fc125833bc2 draft