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comparison miRPlant.xml @ 50:7b5a48b972e9 draft

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author big-tiandm
date Fri, 05 Dec 2014 00:11:02 -0500
parents f008ab2cadc6
children 8b8c356e6db5
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49:f008ab2cadc6 50:7b5a48b972e9
13 <!--command interpreter="perl">miPlant.pl -i $input -format $format -gfa $gfa -idx $index -pre $pre -mat $mat -rfam $rfam -idx2 $idx2 -D $D -a $a -M $M -min $min -max $max -mis $mis -e $e -f $f -v $v -r $r -dis $dis -flank $flank -mfe $mfe -t $t -o $output</command--> 13 <!--command interpreter="perl">miPlant.pl -i $input -format $format -gfa $gfa -idx $index -pre $pre -mat $mat -rfam $rfam -idx2 $idx2 -D $D -a $a -M $M -min $min -max $max -mis $mis -e $e -f $f -v $v -r $r -dis $dis -flank $flank -mfe $mfe -t $t -o $output</command-->
14 14
15 <command interpreter="perl">miRPlant.pl 15 <command interpreter="perl">miRPlant.pl
16 ## Change this to accommodate the number of threads you have available. 16 ## Change this to accommodate the number of threads you have available.
17 -t \${GALAXY_SLOTS:-4} 17 -t \${GALAXY_SLOTS:-4}
18 ## Do or not delet rfam mapped tags
19 #if $params.delet_rfam == "yes":
20 -D
21 #end if
22 -path \$SCRIPT_PATH 18 -path \$SCRIPT_PATH
23 19
24 #for $j, $s in enumerate( $series ) 20 #for $j, $s in enumerate( $series )
25 ##rank_of_series=$j 21 ##rank_of_series=$j
26 -i ${s.input} 22 -i ${s.input}
27 -tag ${s.tag} 23 -tag ${s.tag}
28 #end for 24 #end for
29 25
30 -format $format -gfa $gfa -pre $pre -mat $mat -rfam $rfam -a $a -M $mapnt -min $min -max $max -mis $mismatch -e $e -f $f -v $v -r $r -dis $dis -flank $flank -mfe $mfe > run.log 26 ## prepare bowtie index
27 #set index_path = ''
28 #if str($reference_genome.source) == "history":
29 bowtie-build "$reference_genome.own_file" genome; ln -s "$reference_genome.own_file" genome.fa;
30 #set index_path = 'genome'
31 #else:
32 #set index_path = $reference_genome.index.fields.path
33 #end if
34
35
36 ## Do or not annotate rfam non-miRNA RNAs
37 #if $params.annotate_rfam == "yes":
38
39 ## prepare Rfam bowtie index
40 #set rfam_index_path = ''
41 #if str($params.annotate_rfam.reference_rfam.source) == "history":
42 bowtie-build "$params.annotate_rfam.reference_rfam.own_file" rfam; ln -s "$params.annotate_rfam.reference_rfam.own_file" rfam.fa;
43 #set rfam_index_path = 'rfam'
44 #else:
45 #set rfam_index_path = $params.annotate_rfam.reference_rfam.index.fields.path
46 #end if
47
48 -rfam ${rfam_index_path}.fa -idx2 $rfam_index_path -v $v
49 ## Do or not delet rfam mapped tags
50 #if $params.annotate_rfam.rfamresult.delet_rfam == "yes":
51 -D
52 #end if
53 #end if
54
55
56 ## Do or not annotate known microRNAs
57 #if $params.known_microRNA == "yes":
58 -pre $pre -mat $mat
59 #end if
60
61
62 -format $format -gfa ${index_path}.fa -idx $index_path -phred $phred -a $a -M $mapnt -min $min -max $max -mis $mismatch -e $e -f $f -r $r -dis $dis -flank $flank -mfe $mfe > run.log
31 </command> 63 </command>
32 64
33 <inputs> 65 <inputs>
34 66
35 <repeat name="series" title="Series"> 67 <repeat name="series" title="Series">
36 <param name="input" type="data" label="Raw data"/> 68 <param name="input" type="data" label="Raw data"/>
37 <param name="tag" type="text" data_ref="input" label="Sample name of raw data"/> 69 <param name="tag" type="text" data_ref="input" label="Sample name of raw data"/>
38 </repeat> 70 </repeat>
39 71
72 <conditional name="reference_genome">
73 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
74 <option value="indexed">Use a built-in index</option>
75 <option value="history">Use one from the history</option>
76 </param>
77 <when value="indexed">
78 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
79 <options from_data_table="bowtie_indexes">
80 <filter type="sort_by" column="2"/>
81 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
82 </options>
83 </param>
84 </when>
85 <when value="history">
86 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
87 </when>
88 </conditional>
89
40 <conditional name="params"> 90 <conditional name="params">
41 <param name="delet_rfam" type="select" label="delet rfam mapped reads"> 91 <param name="annotate_rfam" type="select" label="annotate rfam nocoding RNAs(excluding miRNA)">
42 <option value="yes" selected="true">yes</option> 92 <option value="yes" selected="true">yes</option>
43 <option value="no">no</option> 93 <option value="no">no</option>
44 </param> 94 </param>
95 <when value="yes">
96 <!--param name="rfam" type="data" label="rfam sequence file" /-->
97 <conditional name="reference_rfam">
98 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
99 <option value="indexed">Use a built-in index</option>
100 <option value="history">Use one from the history</option>
101 </param>
102 <when value="indexed">
103 <param name="index" type="select" label="Select a reference" help="If your reference of interest is not listed, contact the Galaxy team">
104 <options from_data_table="rfam_bowtie_indexes">
105 <filter type="sort_by" column="2"/>
106 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
107 </options>
108 </param>
109 </when>
110 <when value="history">
111 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference" />
112 </when>
113 </conditional>
114
115 <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches for rfam mapping"/>
116
117 <conditional name="rfamresult">
118 <param name="delet_rfam" type="select" label="delet rfam mapped reads">
119 <option value="yes" selected="true">yes</option>
120 <option value="no">no</option>
121 </param>
122 </conditional> <!-- params -->
123
124
125 </when>
45 </conditional> <!-- params --> 126 </conditional> <!-- params -->
127
46 128
47 <!--param name="input" format="tabular" type="data" label="input config file" /--> 129 <!--param name="input" format="tabular" type="data" label="input config file" /-->
48 130
49 <param name="format" type="select" lable="raw data format" multiple="false"> 131 <param name="format" type="select" lable="raw data format" multiple="false">
50 <option value="fastq">Raw data is fastq. format</option> 132 <option value="fastq">Raw data is fastq. format</option>
51 <option value="fasta">Raw data is fasta. format</option> 133 <option value="fasta">Raw data is fasta. format</option>
52 </param> 134 </param>
53 135
54 <param name="gfa" type="data" label="genome sequence fasta file"/> 136 <param name="phred" type="select" lable="input quals are Phred+64 or Phred+33" multiple="false">
137 <option value="64">Phred+64</option>
138 <option value="33" selected="true">Phred+33</option>
139 </param>
140
141 <conditional name="reference_genome">
142 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
143 <option value="indexed">Use a built-in index</option>
144 <option value="history">Use one from the history</option>
145 </param>
146 <when value="indexed">
147 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
148 <options from_data_table="bowtie_indexes">
149 <filter type="sort_by" column="2"/>
150 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
151 </options>
152 </param>
153 </when>
154 <when value="history">
155 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
156 </when>
157 </conditional>
158
55 <!--param type="data" name="index" label="genome sequence bowtie index"/--> 159 <!--param type="data" name="index" label="genome sequence bowtie index"/-->
56 <param name="mat" type="data" label="mature microRNA sequence file" /> 160 <conditional name="params">
57 <param name="pre" type="data" label="precursor microRNA sequence fie" /> 161 <param name="known_microRNA" type="select" label="Analysis known microRNAs(eg. from mirbase)">
58 <param name="rfam" type="data" label="rfam sequence file" /> 162 <option value="yes" selected="true">yes</option>
163 <option value="no">no</option>
164 </param>
165 <when value="yes">
166 <param name="mat" type="data" label="mature microRNA sequence file" />
167 <param name="pre" type="data" label="precursor microRNA sequence fie" />
168 </when>
169 </conditional> <!-- params -->
170
171 <conditional name="params">
172 <param name="annotate_rfam" type="select" label="annotate rfam nocoding RNAs(excluding miRNA)">
173 <option value="yes" selected="true">yes</option>
174 <option value="no">no</option>
175 </param>
176 <when value="yes">
177 <!--param name="rfam" type="data" label="rfam sequence file" /-->
178 <when value="yes">
179 <!--param name="rfam" type="data" label="rfam sequence file" /-->
180 <conditional name="reference_rfam">
181 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
182 <option value="indexed">Use a built-in index</option>
183 <option value="history">Use one from the history</option>
184 </param>
185 <when value="indexed">
186 <param name="index" type="select" label="Select a reference" help="If your reference of interest is not listed, contact the Galaxy team">
187 <options from_data_table="rfam_bowtie_indexes">
188 <filter type="sort_by" column="2"/>
189 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
190 </options>
191 </param>
192 </when>
193 <when value="history">
194 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference" />
195 </when>
196 </conditional>
197
198 <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches for rfam mapping"/>
199 </when>
200 </conditional> <!-- params -->
201
59 <!--param type="data" name="idx2" label="rfam sequence bowtie index " --> 202 <!--param type="data" name="idx2" label="rfam sequence bowtie index " -->
60 <param name="a" type="text" value="ATCTCGTATG" label="3' adapter sequence" /> 203 <param name="a" type="text" value="ATCTCGTATG" label="3' adapter sequence" />
61 <param name="mapnt" type="integer" value="8" label="minimum adapter map nts" /> 204 <param name="mapnt" type="integer" value="8" label="minimum adapter map nts" />
62 <param name="min" type="integer" value="19" label="minimum microRNA length" /> 205 <param name="min" type="integer" value="19" label="minimum microRNA length" />
63 <param name="max" type="integer" value="28" label="maximum microRNA length" /> 206 <param name="max" type="integer" value="28" label="maximum microRNA length" />
64 <param name="mismatch" type="integer" value="0" label="number of allowed mismatches when mapping reads to precursors" /> 207 <param name="mismatch" type="integer" value="0" label="number of allowed mismatches when mapping reads to precursors" />
65 <param name="e" type="integer" value="2" label="number of nucleotides upstream of the mature sequence to consider" /> 208 <param name="e" type="integer" value="2" label="number of nucleotides upstream of the mature sequence to consider" />
66 <param name="f" type="integer" value="5" label="number of nucleotides downstream of the mature sequence to consider" /> 209 <param name="f" type="integer" value="5" label="number of nucleotides downstream of the mature sequence to consider" />
67 <param name="v" type="integer" value="0" label="report end-to-end hits less than v mismatches"/>
68 <param name="r" type="integer" value="25" label="a read is allowed to map up to this number of positions in the genome" /> 210 <param name="r" type="integer" value="25" label="a read is allowed to map up to this number of positions in the genome" />
69 <param name="dis" type="integer" value="200" label="Maximal space between miRNA and miRNA*" /> 211 <param name="dis" type="integer" value="200" label="Maximal space between miRNA and miRNA*" />
70 <param name="flank" type="integer" value="10" label="Flank sequence length of miRNA precursor" /> 212 <param name="flank" type="integer" value="10" label="Flank sequence length of miRNA precursor" />
71 <param name="mfe" type="float" value="-30" label="Maximal free energy allowed for a miRNA precursor" /> 213 <param name="mfe" type="float" value="-30" label="Maximal free energy allowed for a miRNA precursor" />
72 </inputs> 214 </inputs>
73 215
74 <outputs> 216 <outputs>
75 <data format="txt" name="known microRNA express list" from_work_dir="miRPlant_out/known_microRNA_express.txt" label="${tool.name} on ${on_string}: known microRNA express list"/> 217 <data format="txt" name="known microRNA express list" from_work_dir="miRPlant_out/known_microRNA_express.txt" label="${tool.name} on ${on_string}: known microRNA express list">
76 <data format="txt" name="known microRNA express alignment" from_work_dir="miRPlant_out/known_microRNA_express.aln" label="${tool.name} on ${on_string}: known microRNA express alignment"/> 218 <filter>(params['known_microRNA'] == 'Yes')</filter>
77 <data format="txt" name="known microRNA moRs result" from_work_dir="miRPlant_out/known_microRNA_express.moRs" label="${tool.name} on ${on_string}: known microRNA moRs result"/> 219 </data>
78 <data format="txt" name="known microRNA precursor file" from_work_dir="miRPlant_out/known_microRNA_precursor.fa" label="${tool.name} on ${on_string}: known microRNA precursor file"/> 220 <data format="txt" name="known microRNA express alignment" from_work_dir="miRPlant_out/known_microRNA_express.aln" label="${tool.name} on ${on_string}: known microRNA express alignment">
79 <data format="txt" name="known microRNA mature file" from_work_dir="miRPlant_out/known_microRNA_mature.fa" label="${tool.name} on ${on_string}: known microRNA mature file"/> 221 <filter>(params['known_microRNA'] == 'Yes')</filter>
222 </data>
223 <data format="txt" name="known microRNA moRs result" from_work_dir="miRPlant_out/known_microRNA_express.moRs" label="${tool.name} on ${on_string}: known microRNA moRs result">
224 <filter>(params['known_microRNA'] == 'Yes')</filter>
225 </data>
226 <data format="txt" name="known microRNA precursor file" from_work_dir="miRPlant_out/known_microRNA_precursor.fa" label="${tool.name} on ${on_string}: known microRNA precursor file">
227 <filter>(params['known_microRNA'] == 'Yes')</filter>
228 </data>
229 <data format="txt" name="known microRNA mature file" from_work_dir="miRPlant_out/known_microRNA_mature.fa" label="${tool.name} on ${on_string}: known microRNA mature file">
230 <filter>(params['known_microRNA'] == 'Yes')</filter>
231 </data>
80 <data format="txt" name="novel microRNA express list" from_work_dir="miRPlant_out/novel_microRNA_express.txt" label="${tool.name} on ${on_string}: novel microRNA express list"/> 232 <data format="txt" name="novel microRNA express list" from_work_dir="miRPlant_out/novel_microRNA_express.txt" label="${tool.name} on ${on_string}: novel microRNA express list"/>
81 <data format="txt" name="novel microRNA precursor file" from_work_dir="miRPlant_out/novel_microRNA_precursor.fa" label="${tool.name} on ${on_string}: novel microRNA precursor file"/> 233 <data format="txt" name="novel microRNA precursor file" from_work_dir="miRPlant_out/novel_microRNA_precursor.fa" label="${tool.name} on ${on_string}: novel microRNA precursor file"/>
82 <data format="txt" name="novel microRNA mature sequence file" from_work_dir="miRPlant_out/novel_microRNA_mature.fa" label="${tool.name} on ${on_string}: novel microRNA mature sequence file"/> 234 <data format="txt" name="novel microRNA mature sequence file" from_work_dir="miRPlant_out/novel_microRNA_mature.fa" label="${tool.name} on ${on_string}: novel microRNA mature sequence file"/>
83 <data format="html" name="analysis result" from_work_dir="miRPlant_out/result.html" label="${tool.name} on ${on_string}: analysis result"/> 235 <data format="html" name="analysis result" from_work_dir="miRPlant_out/result.html" label="${tool.name} on ${on_string}: analysis result"/>
84 </outputs> 236 </outputs>