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comparison metaquantome_expand.xml @ 6:767c1d761aaf draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
author galaxyp
date Mon, 18 Mar 2024 12:33:57 +0000
parents 990b4560ead7
children
comparison
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5:4187b6df1a40 6:767c1d761aaf
1 <tool id="metaquantome_expand" name="metaQuantome: expand" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="metaquantome_expand" name="metaQuantome: expand" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>a set of functional or taxonomy annotations</description> 2 <description>a set of functional or taxonomy annotations</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <xml name="FUNC_FILE"> 5 <xml name="FUNC_FILE">
6 <param argument="--func_file" type="data" format="tabular" label="Functional file" 6 <param argument="--func_file" type="data" format="tabular" label="Functional file" help="Tabular file with a peptide sequence column and a functional assignment column with GO terms, EC number, or COG."/>
7 help="Tabular file with a peptide sequence column and a functional assignment column with GO terms, EC number, or COG."/> 7 <param argument="--pep_colname_func" type="text" label="Functional file: peptide column name" value="peptide" help="The column name within the function file that corresponds to the peptide sequences">
8 <param argument="--pep_colname_func" type="text" label="Functional file: peptide column name" value="peptide" 8 <validator type="empty_field"/>
9 help="The column name within the function file that corresponds to the peptide sequences"> 9 </param>
10 <validator type="empty_field"/> 10 </xml>
11 </param> 11 <xml name="FUNC_COLNAME">
12 </xml> 12 <param argument="--func_colname" type="text" label="Functional column name" help="The column name within the function file with the functional terms">
13 <xml name="FUNC_COLNAME"> 13 <validator type="empty_field"/>
14 <param argument="--func_colname" type="text" label="Functional column name" 14 </param>
15 help="The column name within the function file with the functional terms"> 15 </xml>
16 <validator type="empty_field"/> 16 <xml name="TAX_FILE">
17 </param> 17 <param argument="--tax_file" type="data" format="tabular" label="Taxonomy assignments file"/>
18 </xml> 18 <param argument="--pep_colname_tax" type="text" label="Taxonomy file: peptide column name" value="peptide" help="The column name within the taxonomy file that corresponds to the peptide sequences">
19 <xml name="TAX_FILE"> 19 <validator type="empty_field"/>
20 <param argument="--tax_file" type="data" format="tabular" label="Taxonomy assignments file"/> 20 </param>
21 <param argument="--pep_colname_tax" type="text" label="Taxonomy file: peptide column name" value="peptide" 21 </xml>
22 help="The column name within the taxonomy file that corresponds to the peptide sequences"> 22 <xml name="TAX_COLNAME">
23 <validator type="empty_field"/> 23 <param argument="--tax_colname" type="text" label="Taxonomy column name">
24 </param> 24 <help>
25 </xml>
26 <xml name="TAX_COLNAME">
27 <param argument="--tax_colname" type="text" label="Taxonomy column name">
28 <help>
29 Name of column in taxonomy annotation file that contains 25 Name of column in taxonomy annotation file that contains
30 the lowest common ancestor (LCA) annotation. The annotations must 26 the lowest common ancestor (LCA) annotation. The annotations must
31 be either NCBI taxids (strongly preferred) or taxonomy 27 be either NCBI taxids (strongly preferred) or taxonomy
32 names. 28 names.
33 </help> 29 </help>
34 <validator type="empty_field"/> 30 <validator type="empty_field"/>
35 </param> 31 </param>
36 </xml> 32 </xml>
37 <xml name="FT_TAR_RANK"> 33 <xml name="FT_TAR_RANK">
38 <param argument="--ft_tar_rank" type="select" label="rank at which to group taxonomy"> 34 <param argument="--ft_tar_rank" type="select" label="rank at which to group taxonomy">
39 <option value="species">species</option> 35 <option value="species">species</option>
40 <option value="genus" selected="true">genus</option> 36 <option value="genus" selected="true">genus</option>
41 <option value="family">family</option> 37 <option value="family">family</option>
42 <option value="order">order</option> 38 <option value="order">order</option>
43 <option value="class">class</option> 39 <option value="class">class</option>
44 <option value="phylum">phylum</option> 40 <option value="phylum">phylum</option>
45 <option value="kingdom">kingdom</option> 41 <option value="kingdom">kingdom</option>
46 </param> 42 </param>
47 </xml> 43 </xml>
48 <token name="@FUNC_FILE@"> 44 <token name="@FUNC_FILE@">
49 --func_file='$mode_args.func_file' 45 --func_file='$mode_args.func_file'
50 --pep_colname_func='$mode_args.pep_colname_func' 46 --pep_colname_func='$mode_args.pep_colname_func'
51 </token> 47 </token>
52 <token name="@FUNC_COLNAME@"> 48 <token name="@FUNC_COLNAME@">
53 --func_colname='$mode_args.func_colname' 49 --func_colname='$mode_args.func_colname'
54 </token> 50 </token>
55 <token name="@ONTOLOGY@"> 51 <token name="@ONTOLOGY@">
56 --ontology='$mode_args.ontology_args.ontology' 52 --ontology='$mode_args.ontology_args.ontology'
57 #if $mode_args.ontology_args.ontology == 'go' 53 #if $mode_args.ontology_args.ontology == 'go'
58 #if $mode_args.ontology_args.slim_down 54 #if $mode_args.ontology_args.slim_down
59 --slim_down 55 --slim_down
60 #end if 56 #end if
61 #end if 57 #end if
62 </token> 58 </token>
63 <token name="@TAX_FILE@"> 59 <token name="@TAX_FILE@">
64 --tax_file='$mode_args.tax_file' 60 --tax_file='$mode_args.tax_file'
65 --pep_colname_tax='$mode_args.pep_colname_tax' 61 --pep_colname_tax='$mode_args.pep_colname_tax'
66 </token> 62 </token>
67 <token name="@TAX_COLNAME@"> 63 <token name="@TAX_COLNAME@">
68 --tax_colname='$mode_args.tax_colname' 64 --tax_colname='$mode_args.tax_colname'
69 </token> 65 </token>
70 <token name="@FT_TAR_RANK@"> 66 <token name="@FT_TAR_RANK@">
71 --ft_tar_rank='$mode_args.ft_tar_rank' 67 --ft_tar_rank='$mode_args.ft_tar_rank'
72 </token> 68 </token>
73 </macros> 69 </macros>
74 <expand macro="requirements" /> 70 <expand macro="xrefs"/>
75 <command detect_errors="exit_code"><![CDATA[ 71 <expand macro="requirements"/>
72 <command detect_errors="exit_code"><![CDATA[
76 tar -xf '$db_tar' && 73 tar -xf '$db_tar' &&
77 metaquantome expand 74 metaquantome expand
78 --data_dir ./data 75 --data_dir ./data
79 --samps '$samps' 76 --samps '$samps'
80 --mode '$mode_args.mode' 77 --mode '$mode_args.mode'
95 @TAX_COLNAME@ 92 @TAX_COLNAME@
96 @FT_TAR_RANK@ 93 @FT_TAR_RANK@
97 #end if 94 #end if
98 --outfile='$outfile' 95 --outfile='$outfile'
99 ]]></command> 96 ]]></command>
100 <inputs> 97 <inputs>
101 <param name="db_tar" type="data" format="tar" label="Database Archive File" 98 <param name="db_tar" type="data" format="tar" label="Database Archive File" help="must be created by 'metaQuantome: download'"/>
102 help="must be created by 'metaQuantome: download'"/> 99 <expand macro="SAMPS"/>
103 <expand macro="SAMPS"/> 100 <conditional name="mode_args">
104 <conditional name="mode_args"> 101 <param argument="--mode" type="select" label="Mode">
105 <param argument="--mode" type="select" label="Mode"> 102 <option value="f">Functional analysis</option>
106 <option value="f">Functional analysis</option> 103 <option value="t">Taxonomic analysis</option>
107 <option value="t">Taxonomic analysis</option> 104 <option value="ft">Functional-taxonomic interaction analysis</option>
108 <option value="ft">Functional-taxonomic interaction analysis</option> 105 </param>
106 <when value="f">
107 <expand macro="FUNC_FILE"/>
108 <expand macro="ONTOLOGY_ARGS"/>
109 <expand macro="FUNC_COLNAME"/>
110 </when>
111 <when value="t">
112 <expand macro="TAX_FILE"/>
113 <expand macro="TAX_COLNAME"/>
114 </when>
115 <when value="ft">
116 <expand macro="FUNC_FILE"/>
117 <expand macro="FUNC_COLNAME"/>
118 <expand macro="ONTOLOGY_ARGS"/>
119 <expand macro="TAX_FILE"/>
120 <expand macro="TAX_COLNAME"/>
121 <expand macro="FT_TAR_RANK"/>
122 </when>
123 </conditional>
124 <param argument="--int_file" type="data" format="tabular" label="Intensity file" help=""/>
125 <param argument="--pep_colname_int" type="text" value="peptide" label="Intensity file: peptide column name" help="The column name within the intensity file that corresponds to the peptide sequences">
126 <validator type="empty_field"/>
109 </param> 127 </param>
110 <when value="f"> 128 </inputs>
111 <expand macro="FUNC_FILE"/> 129 <outputs>
112 <expand macro="ONTOLOGY_ARGS"/> 130 <data format="tabular" name="outfile" label="${tool.name} on ${on_string} expanded"/>
113 <expand macro="FUNC_COLNAME"/> 131 </outputs>
114 </when> 132 <tests>
115 <when value="t"> 133 <test>
116 <expand macro="TAX_FILE"/> 134 <param name="db_tar" value="ec.tar" ftype="tar"/>
117 <expand macro="TAX_COLNAME"/> 135 <param name="samps" value="samples_basic.tab" ftype="tabular"/>
118 </when> 136 <param name="int_file" value="int_ttest.tab" ftype="tabular"/>
119 <when value="ft"> 137 <param name="pep_colname_int" value="peptide"/>
120 <expand macro="FUNC_FILE"/> 138 <param name="func_file" value="multiple_func.tab"/>
121 <expand macro="FUNC_COLNAME"/> 139 <param name="pep_colname_func" value="peptide"/>
122 <expand macro="ONTOLOGY_ARGS"/> 140 <param name="func_colname" value="ec"/>
123 <expand macro="TAX_FILE"/> 141 <param name="mode" value="f"/>
124 <expand macro="TAX_COLNAME"/> 142 <param name="ontology" value="ec"/>
125 <expand macro="FT_TAR_RANK"/> 143 <output name="outfile">
126 </when> 144 <assert_contents>
127 </conditional> 145 <has_text text="1.2.7.10"/>
128 <param argument="--int_file" type="data" format="tabular" label="Intensity file" 146 </assert_contents>
129 help=""/> 147 </output>
130 <param argument="--pep_colname_int" type="text" value="peptide" label="Intensity file: peptide column name" 148 </test>
131 help="The column name within the intensity file that corresponds to the peptide sequences"> 149 </tests>
132 <validator type="empty_field"/> 150 <help>
133 </param>
134 </inputs>
135 <outputs>
136 <data format="tabular" name="outfile" label="${tool.name} on ${on_string} expanded"/>
137 </outputs>
138 <tests>
139 <test>
140 <param name="db_tar" value="ec.tar" ftype="tar"/>
141 <param name="samps" value="samples_basic.tab" ftype="tabular"/>
142 <param name="int_file" value="int_ttest.tab" ftype="tabular"/>
143 <param name="pep_colname_int" value="peptide" />
144 <param name="func_file" value="multiple_func.tab" />
145 <param name="pep_colname_func" value="peptide" />
146 <param name="func_colname" value="ec"/>
147 <param name="mode" value="f" />
148 <param name="ontology" value="ec" />
149 <output name="outfile">
150 <assert_contents>
151 <has_text text="1.2.7.10"/>
152 </assert_contents>
153 </output>
154 </test>
155 </tests>
156 <help>
157 <![CDATA[ 151 <![CDATA[
158 metaQuantome expand 152 metaQuantome expand
159 =================== 153 ===================
160 154
161 The *expand* module is the first analysis step in the metaQuantome analysis workflow, 155 The *expand* module is the first analysis step in the metaQuantome analysis workflow,
228 Questions, Comments, Problems, Kudos 222 Questions, Comments, Problems, Kudos
229 ------------------------------------ 223 ------------------------------------
230 224
231 Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues. 225 Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
232 ]]></help> 226 ]]></help>
233 <expand macro="citations" /> 227 <expand macro="citations"/>
234 </tool> 228 </tool>