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comparison porechop.xml @ 8:852b3fe95c20 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/porechop commit aa6136c5fa32b987f64bd2b0dc1f72018038b0bb
author jdv
date Fri, 20 Oct 2017 23:11:21 -0400
parents 18d17a5bfe11
children e3ad639c692a
comparison
equal deleted inserted replaced
7:18d17a5bfe11 8:852b3fe95c20
48 48
49 #end if 49 #end if
50 50
51 ##--Adapter Trim Options-------------------------- 51 ##--Adapter Trim Options--------------------------
52 52
53 #if str($trim_section.trim_options.trim) == "yes": 53 #if str($trim_section.trim) == "no":
54
55 --adapter_threshold $trim_section.trim_options.adapter_threshold
56 --check_reads $trim_section.trim_options.check_reads
57 --scoring_scheme $trim_section.trim_options.scoring_scheme
58
59 --end_size $trim_section.trim_options.end_size
60 --end_threshold $trim_section.trim_options.end_threshold
61 --min_trim_size $trim_section.trim_options.min_trim_size
62 --extra_end_trim $trim_section.trim_options.extra_end_trim
63
64 $trim_section.trim_options.discard_middle
65 --middle_threshold $trim_section.trim_options.middle_threshold
66 --extra_middle_trim_good_side $trim_section.trim_options.extra_middle_trim_good_side
67 --extra_middle_trim_bad_side $trim_section.trim_options.extra_middle_trim_bad_side
68 --min_split_read_size $trim_section.trim_options.min_split_read_size
69
70
71 #else:
72 --untrimmed 54 --untrimmed
73
74 #end if 55 #end if
56
57 --adapter_threshold $adapter_section.adapter_threshold
58 --check_reads $adapter_section.check_reads
59 --scoring_scheme $adapter_section.scoring_scheme
60
61 --end_size $adapter_section.end_size
62 --end_threshold $adapter_section.end_threshold
63 --min_trim_size $adapter_section.min_trim_size
64 --extra_end_trim $adapter_section.extra_end_trim
65
66 $adapter_section.discard_middle
67 --middle_threshold $adapter_section.middle_threshold
68 --extra_middle_trim_good_side $adapter_section.extra_middle_trim_good_side
69 --extra_middle_trim_bad_side $adapter_section.extra_middle_trim_bad_side
70 --min_split_read_size $adapter_section.min_split_read_size
71
75 72
76 | perl $__tool_directory__/porechop_summarize.pl 73 | perl $__tool_directory__/porechop_summarize.pl
77 > $result_table 74 > $result_table
78 75
79 ]]> 76 ]]>
105 </when> 102 </when>
106 </conditional> 103 </conditional>
107 </section> 104 </section>
108 105
109 <section name="trim_section" title="Trimming Options" expanded="True"> 106 <section name="trim_section" title="Trimming Options" expanded="True">
110 <conditional name="trim_options">
111 <param name="trim" type="select" label="Perform adapter trimming" help=""> 107 <param name="trim" type="select" label="Perform adapter trimming" help="">
112 <option value="no" selected="true">no</option> 108 <option value="no" selected="true">no</option>
113 <option value="yes">yes</option> 109 <option value="yes">yes</option>
114 </param> 110 </param>
115 <when value="no" /> 111 </section>
116 <when value="yes"> 112 <section name="adapter_section" title="Adapter Options" expanded="False">
117 <param argument="--adapter_threshold" size="4" type="float" value="90.0" min="0" max="100" label="Adapter set threshold identity" /> 113 <param argument="--adapter_threshold" size="4" type="float" value="90.0" min="0" max="100" label="Adapter set threshold identity" />
118 <param argument="--check_reads" size="7" type="integer" value="10000" label="Number of reads to check to determine adapter sets" /> 114 <param argument="--check_reads" size="7" type="integer" value="10000" label="Number of reads to check to determine adapter sets" />
119 <param argument="--barcode_diff" size="4" type="float" value="5.0" min="0" max="100" label="Barcode threshold difference" /> 115 <param argument="--scoring_scheme" type="text" value="3,-6,-5,-2" label="Scoring scheme" />
120 <param argument="--scoring_scheme" type="text" value="3,-6,-5,-2" label="Scoring scheme" /> 116 <param argument="--end_size" size="4" type="integer" value="150" label="Number of terminal bases to search" />
121 <param argument="--end_size" size="4" type="integer" value="150" label="Number of terminal bases to search" /> 117 <param argument="--min_trim_size" size="4" type="integer" value="4" label="Minimum adapter match length" />
122 <param argument="--min_trim_size" size="4" type="integer" value="4" label="Minimum adapter match length" /> 118 <param argument="--extra_end_trim" size="4" type="integer" value="2" label="Adjacent bases to trim " />
123 <param argument="--extra_end_trim" size="4" type="integer" value="2" label="Adjacent bases to trim " /> 119 <param argument="--end_threshold" size="4" type="float" value="75.0" min="0" max="100" label="End adapter trim threshold identity" />
124 <param argument="--end_threshold" size="4" type="float" value="75.0" min="0" max="100" label="End adapter trim threshold identity" /> 120
125 121 <param argument="--discard_middle" type="boolean" truevalue="--discard_middle" falsevalue="" checked="false" label="Discard reads with middle adapters" />
126 <param argument="--discard_middle" type="boolean" truevalue="--discard_middle" falsevalue="" checked="false" label="Discard reads with middle adapters" /> 122 <param argument="--middle_threshold" size="4" type="float" value="85.0" min="0" max="100" label="Middle adapter trim threshold identity" />
127 <param argument="--middle_threshold" size="4" type="float" value="85.0" min="0" max="100" label="Middle adapter trim threshold identity" /> 123 <param argument="--extra_middle_trim_good_side" size="4" type="integer" value="10" label="Adjacent bases to trim on good side" />
128 <param argument="--extra_middle_trim_good_side" size="4" type="integer" value="10" label="Adjacent bases to trim on good side" /> 124 <param argument="--extra_middle_trim_bad_side" size="4" type="integer" value="100" label="Adjacent bases to trim on bad side" />
129 <param argument="--extra_middle_trim_bad_side" size="4" type="integer" value="100" label="Adjacent bases to trim on bad side" /> 125 <param argument="--min_split_read_size" size="4" type="integer" value="1000" label="Minimum length of split reads to keep" />
130 <param argument="--min_split_read_size" size="4" type="integer" value="1000" label="Minimum length of split reads to keep" />
131 </when>
132 </conditional>
133 </section> 126 </section>
134 127
135 </inputs> 128 </inputs>
136 129
137 <!-- ***************************************************************** --> 130 <!-- ***************************************************************** -->
155 <tests> 148 <tests>
156 <test> 149 <test>
157 <param name="input" value="test_barcodes.fastq" ftype="fastq" /> 150 <param name="input" value="test_barcodes.fastq" ftype="fastq" />
158 <param name="demux" value="yes" /> 151 <param name="demux" value="yes" />
159 <output_collection name="output_collection_fastq" type="list" count="4"> 152 <output_collection name="output_collection_fastq" type="list" count="4">
160 <element name="BC01.fastq" file="bar1/BC01.fastq" compare="diff" decompress="true"/> 153 <element name="BC01" file="bar1/BC01.fastq" compare="diff" decompress="true"/>
161 <element name="BC02.fastq" file="bar1/BC02.fastq" compare="diff" decompress="true"/> 154 <element name="BC02" file="bar1/BC02.fastq" compare="diff" decompress="true"/>
162 <element name="BC03.fastq" file="bar1/BC03.fastq" compare="diff" decompress="true"/> 155 <element name="BC03" file="bar1/BC03.fastq" compare="diff" decompress="true"/>
163 <element name="none.fastq" file="bar1/none.fastq" compare="diff" decompress="true"/> 156 <element name="none" file="bar1/none.fastq" compare="diff" decompress="true"/>
164 </output_collection> 157 </output_collection>
165 </test> 158 </test>
166 <test> 159 <test>
167 <param name="input" value="test_barcodes.fastq" ftype="fastq" /> 160 <param name="input" value="test_barcodes.fastq" ftype="fastq" />
168 <param name="demux" value="yes" /> 161 <param name="demux" value="yes" />
169 <param name="require_two_barcodes" value="True" /> 162 <param name="require_two_barcodes" value="True" />
170 <output_collection name="output_collection_fastq" type="list" count="4"> 163 <output_collection name="output_collection_fastq" type="list" count="4">
171 <element name="BC01.fastq" file="bar2/BC01.fastq" compare="diff" decompress="true"/> 164 <element name="BC01" file="bar2/BC01.fastq" compare="diff" decompress="true"/>
172 <element name="BC02.fastq" file="bar2/BC02.fastq" compare="diff" decompress="true"/> 165 <element name="BC02" file="bar2/BC02.fastq" compare="diff" decompress="true"/>
173 <element name="BC03.fastq" file="bar2/BC03.fastq" compare="diff" decompress="true"/> 166 <element name="BC03" file="bar2/BC03.fastq" compare="diff" decompress="true"/>
174 <element name="none.fastq" file="bar2/none.fastq" compare="diff" decompress="true"/> 167 <element name="none" file="bar2/none.fastq" compare="diff" decompress="true"/>
175 </output_collection> 168 </output_collection>
176 </test> 169 </test>
177 <test> 170 <test>
178 <param name="input" value="test_barcodes.fastq" ftype="fastq" /> 171 <param name="input" value="test_barcodes.fastq" ftype="fastq" />
179 <param name="demux" value="yes" /> 172 <param name="demux" value="yes" />
180 <param name="trim" value="yes" /> 173 <param name="trim" value="yes" />
181 <param name="discard_unassigned" value="yes" /> 174 <param name="discard_unassigned" value="yes" />
182 <output_collection name="output_collection_fastq" type="list" count="3"> 175 <output_collection name="output_collection_fastq" type="list" count="3">
183 <element name="BC01.fastq" file="bar1_trim/BC01.fastq" compare="diff" decompress="true"/> 176 <element name="BC01" file="bar1_trim/BC01.fastq" compare="diff" decompress="true"/>
184 <element name="BC02.fastq" file="bar1_trim/BC02.fastq" compare="diff" decompress="true"/> 177 <element name="BC02" file="bar1_trim/BC02.fastq" compare="diff" decompress="true"/>
185 <element name="BC03.fastq" file="bar1_trim/BC03.fastq" compare="diff" decompress="true"/> 178 <element name="BC03" file="bar1_trim/BC03.fastq" compare="diff" decompress="true"/>
186 </output_collection> 179 </output_collection>
187 </test> 180 </test>
188 </tests> 181 </tests>
189 182
190 <!-- ***************************************************************** --> 183 <!-- ***************************************************************** -->