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comparison meme_chip.xml @ 9:4fc125833bc2 draft

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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
comparison
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8:81c0806236ef 9:4fc125833bc2
1 <tool id="meme_chip" name="MEME-ChIP" version="4.11.2"> 1 <tool id="meme_chip" name="MEME-ChIP" version="@WRAPPER_VERSION@+galaxy1">
2 <description>- motif discovery, enrichment analysis and clustering on large nucleotide datasets</description> 2 <description>- motif discovery, enrichment analysis and clustering on large nucleotide datasets</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
14 -neg '$control' 14 -neg '$control'
15 #end if 15 #end if
16 $sequence_alphabet 16 $sequence_alphabet
17 -o '$output.files_path' 17 -o '$output.files_path'
18 #if str($options_type_cond.options_type)=='advanced': 18 #if str($options_type_cond.options_type)=='advanced':
19 #if str($options_type_cond.run_centrimo_cond.run_centrimo) == "yes": 19 ## FIXME: CentriMo cannot be run, See the comments in the input section.
20 -db $options_type_cond.run_centrimo_cond.meme_motif_databases.fields.path 20 ## #set run_centrimo = $options_type_cond.run_centrimo_cond.run_centrimo
21 #if $options_type_cond.run_centrimo_cond.centrimo_local: 21 ## #if str($run_centrimo) == "yes":
22 -centrimo-local 22 ## -db $options_type_cond.run_centrimo_cond.meme_motif_databases.fields.path
23 #end if 23 ## #if $options_type_cond.run_centrimo_cond.centrimo_local:
24 #if $options_type_cond.run_centrimo_cond.centrimo_score: 24 ## -centrimo-local
25 -centrimo-score $options_type_cond.run_centrimo_cond.centrimo_score 25 ## #end if
26 #end if 26 ## #if $options_type_cond.run_centrimo_cond.centrimo_score:
27 #if $options_type_cond.run_centrimo_cond.centrimo_maxreg: 27 ## -centrimo-score $options_type_cond.run_centrimo_cond.centrimo_score
28 -centrimo-maxreg $options_type_cond.run_centrimo_cond.centrimo_maxreg 28 ## #end if
29 #end if 29 ## #if $options_type_cond.run_centrimo_cond.centrimo_maxreg:
30 #if $options_type_cond.run_centrimo_cond.centrimo_ethresh: 30 ## -centrimo-maxreg $options_type_cond.run_centrimo_cond.centrimo_maxreg
31 -centrimo-ethresh $options_type_cond.run_centrimo_cond.centrimo_ethresh 31 ## #end if
32 #end if 32 ## #if $options_type_cond.run_centrimo_cond.centrimo_ethresh:
33 #if $options_type_cond.run_centrimo_cond.centrimo_noseq: 33 ## -centrimo-ethresh $options_type_cond.run_centrimo_cond.centrimo_ethresh
34 -centrimo-noseq 34 ## #end if
35 #end if 35 ## #if $options_type_cond.run_centrimo_cond.centrimo_noseq:
36 #if $options_type_cond.run_centrimo_cond.centrimo_flip: 36 ## -centrimo-noseq
37 -centrimo-flip 37 ## #end if
38 #end if 38 ## #if $options_type_cond.run_centrimo_cond.centrimo_flip:
39 #end if 39 ## -centrimo-flip
40 ## #end if
41 ## #end if
40 $options_type_cond.search_given_strand 42 $options_type_cond.search_given_strand
41 -order $options_type_cond.background_model_order 43 -order $options_type_cond.background_model_order
42 #if str($options_type_cond.subsampling_cond.subsampling) == "no": 44 #if str($options_type_cond.subsampling_cond.subsampling) == "no":
43 -norand 45 -norand
44 #if $options_type_cond.subsampling_cond.subsampling.seed: 46 #if $options_type_cond.subsampling_cond.subsampling.seed:
77 -dreme-e $options_type_cond.dreme_e 79 -dreme-e $options_type_cond.dreme_e
78 -dreme-m $options_type_cond.dreme_m 80 -dreme-m $options_type_cond.dreme_m
79 -spamo-skip 81 -spamo-skip
80 -fimo-skip 82 -fimo-skip
81 #end if 83 #end if
82 && rm '$output' 84 && mv $primary_output '$output'
83 && ln -s $primary_output '$output'
84 ]]></command> 85 ]]></command>
85 <inputs> 86 <inputs>
86 <param name="input" type="data" format="fasta" label="Primary sequences" help="Nucleotide sequences must have equal length"/> 87 <param name="input" type="data" format="fasta" label="Primary sequences" help="Nucleotide sequences must have equal length"/>
87 <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"/> 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"/>
88 <param name="sequence_alphabet" type="select" label="Sequence alphabet"> 89 <param name="sequence_alphabet" type="select" label="Sequence alphabet">
94 <option value="basic" selected="true">Basic</option> 95 <option value="basic" selected="true">Basic</option>
95 <option value="advanced">Advanced</option> 96 <option value="advanced">Advanced</option>
96 </param> 97 </param>
97 <when value="basic"/> 98 <when value="basic"/>
98 <when value="advanced"> 99 <when value="advanced">
100 <!--
101 FIXME: CentriMo cannot be run since the tool form cannot populate the mem_motif_database select list below.
99 <conditional name="run_centrimo_cond"> 102 <conditional name="run_centrimo_cond">
100 <param name="run_centrimo" type="select" label="Run TOMTOM and CentriMo?"> 103 <param name="run_centrimo" type="select" label="Run TOMTOM and CentriMo?">
101 <option value="yes" selected="true">Yes</option> 104 <option value="yes" selected="true">Yes</option>
102 <option value="no">No</option> 105 <option value="no">No</option>
103 </param> 106 </param>
104 <when value="yes"> 107 <when value="yes">
108
109 We have 2 dynamic select lists here. The first select list (meme_motif_database_dir) is populated from the meme_motif_databases
110 data table. The second select list (meme_motif_database) is dynamically re-rendered whenever the selection in the meme_motif_database_dir
111 select list is changed. This composition used to work (see Examples->Dynamic Options section of
112 https://docs.galaxyproject.org/en/latest/dev/schema.html) but no longer does. We'll have to figure out what is broken in
113 the dynamic options code in ~/parameters/basic.py in order to uncomment this block.
114
105 <param name="meme_motif_database_dir" type="select" label="Select the motifs (DNA)" refresh_on_change="True"> 115 <param name="meme_motif_database_dir" type="select" label="Select the motifs (DNA)" refresh_on_change="True">
106 <options from_data_table="meme_motif_databases"> 116 <options from_data_table="meme_motif_databases">
107 <column name="name" index="1"/>
108 <column name="value" index="2"/>
109 <filter type="sort_by" column="1"/> 117 <filter type="sort_by" column="1"/>
110 <validator type="no_options" message="No MEME motif databases are available for the selected input"/> 118 <validator type="no_options" message="No MEME motif databases are available for the selected input"/>
111 </options> 119 </options>
112 </param> 120 </param>
113 <param name="meme_motif_database" type="select" label="MEME motif database" dynamic_options="get_meme_motif_database_options(file_path=meme_motif_database_dir)"/> 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)"/>
118 <param name="centrimo_noseq" type="boolean" truevalue="true" falsevalue="" checked="False" label="Store CentriMo sequence IDs in the output"/> 126 <param name="centrimo_noseq" type="boolean" truevalue="true" falsevalue="" checked="False" label="Store CentriMo sequence IDs in the output"/>
119 <param name="centrimo_flip" type="boolean" truevalue="true" falsevalue="" checked="False" label="Reflect CentriMo matches on reverse strand around center"/> 127 <param name="centrimo_flip" type="boolean" truevalue="true" falsevalue="" checked="False" label="Reflect CentriMo matches on reverse strand around center"/>
120 </when> 128 </when>
121 <when value="no"/> 129 <when value="no"/>
122 </conditional> 130 </conditional>
131 -->
123 <param name="background_model_order" type="select" label="Select the order of the Markov background model"> 132 <param name="background_model_order" type="select" label="Select the order of the Markov background model">
124 <option value="0">0-order model of sequences</option> 133 <option value="0">0-order model of sequences</option>
125 <option value="1" selected="True">1st order model of sequences</option> 134 <option value="1" selected="True">1st order model of sequences</option>
126 <option value="2">2nd order model of sequences</option> 135 <option value="2">2nd order model of sequences</option>
127 <option value="3">3rd order model of sequences</option> 136 <option value="3">3rd order model of sequences</option>