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comparison presto_parseheaders.xml @ 0:90315cb06d06 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
author iuc
date Wed, 30 May 2018 15:36:08 -0400
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children 55e95d8104f2
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-1:000000000000 0:90315cb06d06
1 <tool id="presto_parseheaders" name="pRESTO ParseHeaders" version="@PRESTO_VERSION@">
2 <description>Manage annotations in FASTQ headers.</description>
3
4 <macros>
5 <import>presto_macros.xml</import>
6 </macros>
7
8 <expand macro="requirements"/>
9
10 <version_command>ParseHeaders.py --version</version_command>
11 <command detect_errors="exit_code"><![CDATA[
12 ln -s '$fastq_in' in.fastq &&
13 ParseHeaders.py $cc.command
14 -s in.fastq
15
16 #if $varExists('cc.f')
17 -f $cc.f
18 #end if
19 #if $varExists('cc.u')
20 -u $cc.u
21 #end if
22 #if $varExists('cc.act')
23 --act $cc.act
24 #end if
25 #if $varExists('cc.k')
26 -k $cc.k
27 #end if
28
29 --outdir=.
30 --outname=tmp &&
31 mv ./tmp_*header* '$output'
32 ]]></command>
33
34 <inputs>
35 <param name="fastq_in" type="data" format="fastq" label="Input FASTQ file"/>
36
37 <conditional name="cc">
38 <param name="command" type="select" label="Command">
39 <option value="add">Add field/value pairs to header annotations (add)</option>
40 <option value="collapse">Collapse header annotations with multiple entries (collapse)</option>
41 <option value="copy">Copy header annotation fields (copy)</option>
42 <option value="delete">Delete fields from header annotations (delete)</option>
43 <option value="expand">Expand annotation fields with multiple values (expand)</option>
44 <option value="rename">Rename header annotation fields (rename)</option>
45 <option value="table">Write sequence headers to a table (table)</option>
46 </param>
47 <when value="add">
48 <param argument="-f" type="text" value="" label="Field(s)" help="Space-separated list of field names to add.">
49 <expand macro="text-regex-validator"/>
50 </param>
51 <param argument="-u" type="text" value="" label="Value(s)" help="Space-separated list of values, one per field.">
52 <expand macro="text-regex-validator"/>
53 </param>
54 </when>
55 <when value="collapse">
56 <param argument="-f" type="text" value="" label="Field(s)" help="Space-separated list of field names to collapse values within.">
57 <expand macro="text-regex-validator"/>
58 </param>
59 <param argument="--act" type="text" value="" label="Action(s)" help="Space-separated list of actions, one per field [min,max,sum,first,last,set,cat].">
60 <expand macro="text-regex-validator"/>
61 </param>
62 </when>
63 <when value="copy">
64 <param argument="-f" type="text" value="" label="Source Field(s)" help="Space-separated list of field names to copy.">
65 <expand macro="text-regex-validator"/>
66 </param>
67 <param argument="-k" type="text" value="" label="Target Field(s)" help="Space-separated list of target field names, one per source field.">
68 <expand macro="text-regex-validator"/>
69 </param>
70 <param argument="--act" type="text" value="" label="Action(s)" help="Space-separated list of actions, one per target field [min,max,sum,first,last,set,cat].">
71 <expand macro="text-regex-validator"/>
72 </param>
73 </when>
74 <when value="delete">
75 <param argument="-f" type="text" value="" label="Field(s)" help="Space-separated list of field names to delete.">
76 <expand macro="text-regex-validator"/>
77 </param>
78 </when>
79 <when value="expand">
80 <param argument="-f" type="text" value="" label="Field(s)" help="Space-separated list of field names to expand.">
81 <expand macro="text-regex-validator"/>
82 </param>
83 </when>
84 <when value="rename">
85 <param argument="-f" type="text" value="" label="Source Field(s)" help="Space-separated list of field names to rename.">
86 <expand macro="text-regex-validator"/>
87 </param>
88 <param argument="-k" type="text" value="" label="Target Field(s)" help="Space-separated list of new field names.">
89 <expand macro="text-regex-validator"/>
90 </param>
91 <param argument="--act" type="text" value="" label="Action(s)" help="Space-separated list of actions, one per new field [min,max,sum,first,last,set,cat].">
92 <expand macro="text-regex-validator"/>
93 </param>
94 </when>
95 <when value="table">
96 <param argument="-f" type="text" value="" label="Field(s)" help="Space-separated list of field names to report on.">
97 <expand macro="text-regex-validator"/>
98 </param>
99 </when>
100 </conditional>
101 </inputs>
102
103 <outputs>
104 <data name="output" format="fastq">
105 <change_format>
106 <when input="command" value="table" format="tsv"/>
107 </change_format>
108 </data>
109 </outputs>
110
111 <tests>
112 <test>
113 <param name="command" value="add"/>
114 <param name="fastq_in" value="presto_parseheaders_test_in.fastq"/>
115 <param name="f" value="FOO BAR"/>
116 <param name="u" value="hello world"/>
117 <output name="output" file="presto_parseheaders_test_add_out.fastq" sort="true"/>
118 </test>
119
120 <test>
121 <param name="command" value="collapse"/>
122 <param name="fastq_in" value="presto_parseheaders_test_in.fastq"/>
123 <param name="f" value="CONSCOUNT"/>
124 <param name="act" value="sum"/>
125 <output name="output" file="presto_parseheaders_test_collapse_out.fastq" sort="true"/>
126 </test>
127
128 <test>
129 <param name="command" value="copy"/>
130 <param name="fastq_in" value="presto_parseheaders_test_in.fastq"/>
131 <param name="f" value="PRCONS"/>
132 <param name="k" value="PRIMER"/>
133 <param name="act" value="set"/>
134 <output name="output" file="presto_parseheaders_test_copy_out.fastq" sort="true"/>
135 </test>
136
137 <test>
138 <param name="command" value="delete"/>
139 <param name="fastq_in" value="presto_parseheaders_test_in.fastq"/>
140 <param name="f" value="CONSCOUNT SEQORIENT"/>
141 <output name="output" file="presto_parseheaders_test_delete_out.fastq" sort="true"/>
142 </test>
143
144 <test>
145 <param name="command" value="expand"/>
146 <param name="fastq_in" value="presto_parseheaders_test_in.fastq"/>
147 <param name="f" value="CONSCOUNT"/>
148 <output name="output" file="presto_parseheaders_test_expand_out.fastq" sort="true"/>
149 </test>
150
151 <test>
152 <param name="command" value="rename"/>
153 <param name="fastq_in" value="presto_parseheaders_test_in.fastq"/>
154 <param name="f" value="PRCONS"/>
155 <param name="k" value="PRIMER"/>
156 <param name="act" value="set"/>
157 <output name="output" file="presto_parseheaders_test_rename_out.fastq" sort="true"/>
158 </test>
159
160 <test>
161 <param name="command" value="table"/>
162 <param name="fastq_in" value="presto_parseheaders_test_in.fastq"/>
163 <param name="f" value="PRCONS PRIMER"/>
164 <output name="output" file="presto_parseheaders_test_table_out.tsv" sort="true"/>
165 </test>
166 </tests>
167
168 <help><![CDATA[
169 Adds, removes, renames and otherwise transforms annotations in FASTQ headers.
170
171 See the `pRESTO online help <@PRESTO_URL_BASE@/ParseHeaders.html>`_ for more information.
172
173 @HELP_NOTE@
174 ]]></help>
175 <expand macro="citations" />
176 </tool>