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comparison sickle.xml @ 1:43e081d32f90 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015
author iuc
date Sun, 06 Dec 2015 11:31:57 -0500
parents a5f56370e870
children 013275060443
comparison
equal deleted inserted replaced
0:a5f56370e870 1:43e081d32f90
45 #else if $readtype.input_paired1.ext == "fastqsolexa": 45 #else if $readtype.input_paired1.ext == "fastqsolexa":
46 -t solexa 46 -t solexa
47 #end if 47 #end if
48 #end if 48 #end if
49 49
50 #if str($readtype.single_or_paired) == "pe_collection":
51 pe -f "${readtype.input_paired.forward}" -r "${readtype.input_paired.reverse}" -o "${output_paired_coll.forward}" -p "${output_paired_coll.reverse}" -s "$output_paired_coll_single"
52
53 #if $readtype.input_paired.forward.ext in ("fastq", "fastqsanger"):
54 -t sanger
55 #else if $readtype.input_paired.forward.ext == "fastqillumina":
56 -t illumina
57 #else if $readtype.input_paired.forward.ext == "fastqsolexa":
58 -t solexa
59 #end if
60 #end if
61
50 #if str($qual_threshold) != "": 62 #if str($qual_threshold) != "":
51 -q $qual_threshold 63 -q $qual_threshold
52 #end if 64 #end if
53 65
54 #if str($length_threshold) != "": 66 #if str($length_threshold) != "":
68 <conditional name="readtype"> 80 <conditional name="readtype">
69 <param name="single_or_paired" type="select" label="Single-end or paired-end reads?" help="Note: Sickle will infer the quality type of the file from its datatype. I.e., if the datatype is fastqsanger, then the quality type is sanger. The default is fastqsanger."> 81 <param name="single_or_paired" type="select" label="Single-end or paired-end reads?" help="Note: Sickle will infer the quality type of the file from its datatype. I.e., if the datatype is fastqsanger, then the quality type is sanger. The default is fastqsanger.">
70 <option value="se" selected="true">Single-end</option> 82 <option value="se" selected="true">Single-end</option>
71 <option value="pe_combo">Paired-end (one interleaved input file)</option> 83 <option value="pe_combo">Paired-end (one interleaved input file)</option>
72 <option value="pe_sep">Paired-end (two separate input files)</option> 84 <option value="pe_sep">Paired-end (two separate input files)</option>
85 <option value="pe_collection">Paired-end (as collection)</option>
73 </param> 86 </param>
74 87
75 <when value="se"> 88 <when value="se">
76 <param format="fastq" name="input_single" type="data" label="Single-end FASTQ reads" help="(-f)" /> 89 <param format="fastq" name="input_single" type="data" label="Single-end FASTQ reads" help="(-f)" />
77 </when> 90 </when>
83 96
84 <when value="pe_sep"> 97 <when value="pe_sep">
85 <param format="fastq" name="input_paired1" type="data" label="Paired-end forward strand FASTQ reads" help="(-f)" /> 98 <param format="fastq" name="input_paired1" type="data" label="Paired-end forward strand FASTQ reads" help="(-f)" />
86 <param format="fastq" name="input_paired2" type="data" label="Paired-end reverse strand FASTQ reads" help="(-r)" /> 99 <param format="fastq" name="input_paired2" type="data" label="Paired-end reverse strand FASTQ reads" help="(-r)" />
87 </when> 100 </when>
101
102 <when value="pe_collection">
103 <param format="fastq" name="input_paired" type="data_collection" collection_type="paired" label="Paired-end FASTQ reads as paired collection" />
104 </when>
88 </conditional> 105 </conditional>
89 106
90 <param name="qual_threshold" value="20" min="0" type="integer" optional="true" label="Quality threshold" help="Threshold for trimming based on average quality in a window (-q)" /> 107 <param name="qual_threshold" value="20" min="0" type="integer" optional="true" label="Quality threshold" help="Threshold for trimming based on average quality in a window (-q)" />
91 108
92 <param name="length_threshold" value="20" min="0" type="integer" optional="true" label="Length threshold" help="Threshold to keep a read based on length after trimming (-l)" /> 109 <param name="length_threshold" value="20" min="0" type="integer" optional="true" label="Length threshold" help="Threshold to keep a read based on length after trimming (-l)" />
117 </data> 134 </data>
118 135
119 <data name="output_paired_single" format_source="input_paired1" label="Singletons from paired-end output of ${tool.name} on ${on_string}"> 136 <data name="output_paired_single" format_source="input_paired1" label="Singletons from paired-end output of ${tool.name} on ${on_string}">
120 <filter>readtype['single_or_paired'] == 'pe_sep'</filter> 137 <filter>readtype['single_or_paired'] == 'pe_sep'</filter>
121 </data> 138 </data>
139
140 <collection name="output_paired_coll" type="paired" structured_like="input_paired" inherit_format="true" label="Paired-end output of ${tool.name} on ${on_string}">
141 <filter>readtype['single_or_paired'] == 'pe_collection'</filter>
142 </collection>
143
144 <data name="output_paired_coll_single" format_source="input_paired['forward']" label="Singletons from paired-end output of ${tool.name} on ${on_string}">
145 <filter>readtype['single_or_paired'] == 'pe_collection'</filter>
146 </data>
122 </outputs> 147 </outputs>
123 <tests> 148 <tests>
124 <test> 149 <test>
125 <param name="single_or_paired" value="pe_combo" /> 150 <param name="single_or_paired" value="pe_combo" />
126 <param name="input_combo" value="test.fastq" /> 151 <param name="input_combo" ftype="fastqsanger" value="test.fastq" />
127 <param name="qual_threshold" value="34" /> 152 <param name="qual_threshold" value="34" />
128 <output name="output_combo" file="output.c1.fastq" /> 153 <output name="output_combo" ftype="fastqsanger" file="output.c1.fastq" />
129 <output name="output_combo_single" file="output.s.fastq" /> 154 <output name="output_combo_single" ftype="fastqsanger" file="output.s.fastq" />
130 </test> 155 </test>
131 <test> 156 <test>
132 <param name="single_or_paired" value="pe_combo" /> 157 <param name="single_or_paired" value="pe_combo" />
133 <param name="input_combo" value="test.fastq" /> 158 <param name="input_combo" ftype="fastqsanger" value="test.fastq" />
134 <param name="qual_threshold" value="34" /> 159 <param name="qual_threshold" value="34" />
135 <param name="output_n" value="true" /> 160 <param name="output_n" value="true" />
136 <output name="output_combo" file="output.c2.fastq" /> 161 <output name="output_combo" ftype="fastqsanger" file="output.c2.fastq" />
137 </test> 162 </test>
138 <test> 163 <test>
139 <param name="single_or_paired" value="pe_sep" /> 164 <param name="single_or_paired" value="pe_sep" />
140 <param name="input_paired1" value="test.f.fastq" /> 165 <param name="input_paired1" ftype="fastqsanger" value="test.f.fastq" />
141 <param name="input_paired2" value="test.r.fastq" /> 166 <param name="input_paired2" ftype="fastqsanger" value="test.r.fastq" />
142 <param name="qual_threshold" value="34" /> 167 <param name="qual_threshold" value="34" />
143 <output name="output_paired1" file="output.f.fastq" /> 168 <output name="output_paired1" ftype="fastqsanger" file="output.f.fastq" />
144 <output name="output_paired2" file="output.r.fastq" /> 169 <output name="output_paired2" ftype="fastqsanger" file="output.r.fastq" />
145 <output name="output_paired_single" file="output.s.fastq" /> 170 <output name="output_paired_single" ftype="fastqsanger" file="output.s.fastq" />
171 </test>
172 <test>
173 <param name="single_or_paired" value="pe_collection" />
174 <param name="input_paired">
175 <collection type="paired">
176 <element name="forward" ftype="fastqsanger" value="test.f.fastq" />
177 <element name="reverse" ftype="fastqsanger" value="test.r.fastq" />
178 </collection>
179 </param>
180 <param name="qual_threshold" value="34" />
181 <output_collection name="output_paired_coll" type="paired">
182 <element name="forward" ftype="fastqsanger" file="output.f.fastq" />
183 <element name="reverse" ftype="fastqsanger" file="output.r.fastq" />
184 </output_collection>
185 <output name="output_paired_coll_single" ftype="fastqsanger" file="output.s.fastq" />
146 </test> 186 </test>
147 </tests> 187 </tests>
148 <help> 188 <help>
149 **What it does** 189 **What it does**
150 190