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comparison macros.xml.orig @ 4:d5d44f7d6e4a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 07:50:49 +0000
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3:1221f80947f4 4:d5d44f7d6e4a
1 <?xml version="1.0"?>
2 <macros>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="@TOOL_VERSION@">obitools</requirement>
6 </requirements>
7 </xml>
8 <<<<<<< HEAD
9
10 <token name="@TOOL_VERSION@">1.2.13</token>
11 <token name="@PROFILE@">21.01</token>
12 =======
13 <xml name="bio_tools">
14 <xrefs>
15 <xref type='bio.tools'>obitools</xref>
16 </xrefs>
17 </xml>
18 <token name="@TOOL_VERSION@">1.2.11</token>
19 >>>>>>> 7abad681f (add tools up until P)
20
21 <xml name="stdio">
22 <stdio>
23 <exit_code range="1:" level="fatal" description="Error in Obitools execution" />
24 </stdio>
25 </xml>
26
27 <token name="@INPUT_FORMATS@">fastqsanger,fastqsanger.gz,fastqsolexa,fastqsolexa.gz,fasta,fasta.gz</token>
28 <token name="@GUNZIP_INPUT@"><![CDATA[
29 #if $input.ext.endswith(".gz")
30 gunzip -c '$input' > input &&
31 #else
32 ln -s '$input' input &&
33 #end if
34 ]]></token>
35 <token name="@GZIP_OUTPUT@"><![CDATA[
36 #if $input.ext.endswith(".gz")
37 | gzip -c
38 #end if
39 ]]></token>
40
41 <!-- generate galaxy.json to determine output format
42 - by default same as input
43 - if out_format can be specified
44 - fasta/fastq depending on $out_format (if != "")
45 - or fasta if the tool does not support choosing the output format, e.g. obiuniq which always outputs fasta
46 - gz if $input is zipped
47
48 A list of outputs to include in the json can be given by
49 setting a variable $outputs = [...] listing pairs of output names and the actual output
50 (defaults to [("output", $output)])
51 -->
52 <token name="@GENERATE_GALAXY_JSON@"><![CDATA[
53 #import json
54
55 #try:
56 #silent $outputs[0]
57 #except
58 #set outputs = [("output", $output)]
59 #end try
60
61 #if $input.ext.startswith("fastq")
62 #set ext = "fastqsanger"
63 #else if $input.ext.startswith("fasta")
64 #set ext = "fasta"
65 #end if
66
67 #try
68 #if $out_format == "fasta"
69 #set ext = "fasta"
70 #else if $out_format == "fastq"
71 #set ext = "fastqsanger"
72 #end if
73 #except
74 #set ext = "fasta"
75 #end try
76
77 #if $input.ext.endswith(".gz")
78 #set ext = ext + ".gz"
79 #end if
80
81 #set gxy_json = {}
82 #for oname, o in $outputs
83 #silent gxy_json[oname] = {"ext": ext}
84 #end for
85 && echo '${json.dumps(gxy_json)}' >> galaxy.json
86 ]]></token>
87
88 <token name="@OUT_FORMAT@"><![CDATA[
89 #if $out_format
90 --${out_format}-output
91 #end if
92 ]]></token>
93
94 <xml name="out_format_macro">
95 <param name="out_format" type="select" optional="true" label="Output data type" help="For FASTA/Q the the default output type is the same as the input type">
96 <option value="fasta">fasta</option>
97 <option value="fastq">fastq</option>
98 </param>
99 </xml>
100
101 <token name="@OBITOOLS_LINK@">
102 <![CDATA[
103 --------
104
105 **Project links:**
106
107 `OBITools`_
108
109 .. _OBITools: https://pythonhosted.org/OBITools/
110 ]]>
111 </token>
112
113 <xml name="attributes">
114 <option value="ali_dir" selected="true">ali_dir</option>
115 <option value="ali_length">ali_length</option>
116 <option value="avg_quality">avg_quality</option>
117 <option value="best_match">best_match</option>
118 <option value="best_identity">best_identity</option>
119 <option value="class">class</option>
120 <option value="cluster">cluster</option>
121 <option value="complemented">complemented</option>
122 <option value="count">count</option>
123 <option value="cut">cut</option>
124 <option value="direction">direction</option>
125 <option value="distance">distance</option>
126 <option value="error">error</option>
127 <option value="experiment">experiment</option>
128 <option value="family">family</option>
129 <option value="family_name">family_name</option>
130 <option value="forward_error">forward_error</option>
131 <option value="forward_match">forward_match</option>
132 <option value="forward_primer">forward_primer</option>
133 <option value="forward_score">forward_score</option>
134 <option value="forward_tag">forward_tag</option>
135 <option value="forward_tm">forward_tm</option>
136 <option value="genus">genus</option>
137 <option value="genus_name">genus_name</option>
138 <option value="head_quality">head_quality</option>
139 <option value="id_status">id_status</option>
140 <option value="merged_star">merged_star</option>
141 <option value="merged">merged</option>
142 <option value="mid_quality">mid_quality</option>
143 <option value="mode">mode</option>
144 <option value="obiclean_cluster">obiclean_cluster</option>
145 <option value="obiclean_count">obiclean_count</option>
146 <option value="obiclean_head">obiclean_head</option>
147 <option value="obiclean_headcount">obiclean_headcount</option>
148 <option value="obiclean_internalcount">obiclean_internalcount</option>
149 <option value="obiclean_samplecount">obiclean_samplecount</option>
150 <option value="obiclean_singletoncount">obiclean_singletoncount</option>
151 <option value="obiclean_status">obiclean_status</option>
152 <option value="occurrence">occurrence</option>
153 <option value="order">order</option>
154 <option value="order_name">order_name</option>
155 <option value="pairend_limit ">pairend_limit </option>
156 <option value="partial ">partial </option>
157 <option value="rank">rank</option>
158 <option value="reverse_error">reverse_error</option>
159 <option value="reverse_match">reverse_match</option>
160 <option value="reverse_primer">reverse_primer</option>
161 <option value="reverse_score">reverse_score</option>
162 <option value="reverse_tag">reverse_tag</option>
163 <option value="reverse_tm">reverse_tm</option>
164 <option value="sample">sample</option>
165 <option value="scientific_name">scientific_name</option>
166 <option value="score">score</option>
167 <option value="score_norm">score_norm</option>
168 <option value="select">select</option>
169 <option value="seq_ab_match">seq_ab_match</option>
170 <option value="seq_a_single">seq_a_single</option>
171 <option value="seq_a_mismatch">seq_a_mismatch</option>
172 <option value="seq_a_deletion">seq_a_deletion</option>
173 <option value="seq_a_insertion">seq_a_insertion</option>
174 <option value="seq_b_single">seq_b_single</option>
175 <option value="seq_b_mismatch">seq_b_mismatch</option>
176 <option value="seq_b_deletion">seq_b_deletion</option>
177 <option value="seq_b_insertion">seq_b_insertion</option>
178 <option value="seq_length">seq_length</option>
179 <option value="seq_length_ori">seq_length_ori</option>
180 <option value="seq_rank">seq_rank</option>
181 <option value="sminL">sminL</option>
182 <option value="sminR">sminR</option>
183 <option value="species">species</option>
184 <option value="species_list">species_list</option>
185 <option value="species_name">species_name</option>
186 <option value="status">status</option>
187 <option value="strand">strand</option>
188 <option value="tail_quality">tail_quality</option>
189 <option value="taxid">taxid</option>
190 </xml>
191
192 <xml name="input_format_options_macro">
193 <section name="input_format_options" title="Input format options" expanded="false">
194 <param name="options_inputtype" type="select" optional="true" label="Specify the input datatype" help="default: determine automatically (should only be necessay for non FASTA/FASTQ datasets)">
195 <option value="--genbank">genbank</option>
196 <option value="--embl">embl</option>
197 <option value="--sanger">sanger</option>
198 <option value="--solexa">solexa</option>
199 <option value="--ecopcr">ecopcr</option>
200 <option value="--ecopcrdb">ecopcrdb</option>
201 <option value="--fasta">fasta (including obitools fasta extentions)</option>
202 <option value="--raw-fasta">raw fasta (more tolerant format variant)</option>
203 </param>
204 <param name="options_seqtype" type="select" optional="true" label="Specify the sequence datatype" >
205 <option value="--nuc">nucleic</option>
206 <option value="--prot">protein</option>
207 </param>
208 </section>
209 </xml>
210
211 <token name="@INPUT_FORMAT@"><![CDATA[
212 #if $input_format_options.options_inputtype
213 $input_format_options.options_inputtype
214 #else
215 #if $input.ext.startswith("fasta")
216 --fasta
217 #else if $input.ext.startswith("fastqsolexa")
218 ## input file is in fastq nucleic format produced by solexa sequencer
219 --solexa
220 #else
221 ## input file is in sanger fastq nucleic format (standard fastq)
222 --sanger
223 #end if
224 #end if
225 #if $input_format_options.options_seqtype
226 $input_format_options.options_seqtype
227 #end if
228 ]]></token>
229
230 <xml name="sanitizer">
231 <sanitizer invalid_char="test">
232 <valid initial="default">
233 <!--add value="&quot;"/-->
234 </valid>
235 <mapping initial="default">
236 <add source="&gt;" target="\&gt;"/>
237 <add source="&quot;" target="\&quot;"/>
238 </mapping>
239 </sanitizer>
240 </xml>
241
242 <xml name="citation">
243 <citations>
244 <citation type="doi">10.1111/1755-0998.12428</citation>
245 </citations>
246 </xml>
247
248 </macros>