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comparison cmscan.xml @ 9:1d74ed49cf41 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 09c1d4ab75f5cd057ed57bf694217f0e355f785e
author bgruening
date Mon, 11 Nov 2024 10:27:19 +0000
parents c9e29ac5d099
children
comparison
equal deleted inserted replaced
8:c9e29ac5d099 9:1d74ed49cf41
1 <tool id="infernal_cmscan" name="cmscan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="infernal_cmscan" name="cmscan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description> Search sequences against collections of covariance models</description> 2 <description> Search sequences against collections of covariance models</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="xrefs"/>
6 <expand macro="requirements"/> 7 <expand macro="requirements"/>
7 <expand macro="stdio"/> 8 <expand macro="stdio"/>
8 <expand macro="xrefs"/> 9 <command detect_errors="aggressive">
9 <command>
10 <![CDATA[ 10 <![CDATA[
11 ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy 11 ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
12 ## it will be converted to a tab delimited file and piped to Galaxy 12 ## it will be converted to a tab delimited file and piped to Galaxy
13 temp_tabular_output=\$(mktemp) && 13 temp_tabular_output=\$(mktemp) &&
14 14
15 #if str($cm_opts.cm_opts_selector) == "histdb": 15 #if str($cm_opts.cm_opts_selector) == "histdb":
16 ln -s '$cm_opts.cmfile' cmdb.cm && 16 ln -s '$cm_opts.cmfile' cmdb.cm
17 #else:
18 ln -s '$cm_opts.database.fields.path' cmdb.cm
17 #end if 19 #end if
18 20 &&
19 tar xvf '$aux_files' && 21 tar xvf '$aux_files' &&
20 ln -s `find *.i1f` cmdb.cm.i1f && 22 ln -s `find *.i1f` cmdb.cm.i1f &&
21 ln -s `find *.i1i` cmdb.cm.i1i && 23 ln -s `find *.i1i` cmdb.cm.i1i &&
22 ln -s `find *.i1m` cmdb.cm.i1m && 24 ln -s `find *.i1m` cmdb.cm.i1m &&
23 ln -s `find *.i1p` cmdb.cm.i1p && 25 ln -s `find *.i1p` cmdb.cm.i1p &&
64 #if $acceleration_huristics.acceleration_huristics_selector == "--mid" 66 #if $acceleration_huristics.acceleration_huristics_selector == "--mid"
65 --Fmid $acceleration_huristics.Fmid 67 --Fmid $acceleration_huristics.Fmid
66 #end if 68 #end if
67 #end if 69 #end if
68 ## CM file from the history or stored as database on disc 70 ## CM file from the history or stored as database on disc
69 #if str($cm_opts.cm_opts_selector) == "db": 71 cmdb.cm
70 '$cm_opts.database.fields.path'
71 #else:
72 ##'$cm_opts.cmfile'
73 cmdb.cm
74 #end if
75 ## sequence file 72 ## sequence file
76 '$seqdb' 73 '$seqdb'
77 ######### Parse the output file in order to fix a problem reported in https://help.galaxyproject.org/t/messy-infernal-cmscan-output/5984 74 ######### Parse the output file in order to fix a problem reported in https://help.galaxyproject.org/t/messy-infernal-cmscan-output/5984
78 ## remove the header 75 ## remove the header
79 && tail -n +3 '\$temp_tabular_output' > headless_file 76 && tail -n +3 '\$temp_tabular_output' > headless_file
90 87
91 ]]> 88 ]]>
92 </command> 89 </command>
93 <inputs> 90 <inputs>
94 <param name="seqdb" type="data" format="fasta" label="Sequence database &lt;seqfile&gt;"/> 91 <param name="seqdb" type="data" format="fasta" label="Sequence database &lt;seqfile&gt;"/>
95 92 <expand macro="DB" />
96 <conditional name="cm_opts">
97 <param name="cm_opts_selector" type="select" label="Subject covariance models &lt;cmdb&gt; ">
98 <option value="db" >Locally installed covariance models</option>
99 <option value="histdb" selected="True">Covariance model from your history</option>
100 </param>
101 <when value="db">
102 <param name="database" type="select" label="Covariance models">
103 <options from_file="infernal.loc">
104 <column name="value" index="0"/>
105 <column name="name" index="1"/>
106 <column name="path" index="2"/>
107 </options>
108 </param>
109 </when>
110 <when value="histdb">
111 <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/>
112 </when>
113 </conditional>
114 <param name="aux_files" type="data" format="tar" label="Auxillury files" help="A tar file contains the four auxillury files suffixed .i1{fimp}. These files are generated after pressing the cm files using cmpress"/> 93 <param name="aux_files" type="data" format="tar" label="Auxillury files" help="A tar file contains the four auxillury files suffixed .i1{fimp}. These files are generated after pressing the cm files using cmpress"/>
115 94
116 <param argument="-g" truevalue="-g" falsevalue="" checked="False" type="boolean" 95 <param argument="-g" truevalue="-g" falsevalue="" checked="False" type="boolean"
117 label="Turn on the glocal alignment algorithm" help="... global with respect to the query model and local with respect to the target database."/> 96 label="Turn on the glocal alignment algorithm" help="... global with respect to the query model and local with respect to the target database."/>
118 <param argument="-Z" type="float" optional="true" min="0" label="Search space size in *Mb* for E-value calculations" help="Without the use of this option, the search space size changes for each query sequence"/> 97 <param argument="-Z" type="float" optional="true" min="0" label="Search space size in *Mb* for E-value calculations" help="Without the use of this option, the search space size changes for each query sequence"/>
256 <has_n_lines n="15"/> 235 <has_n_lines n="15"/>
257 <has_text text="AAGA01015927.1"/> 236 <has_text text="AAGA01015927.1"/>
258 </assert_contents> 237 </assert_contents>
259 </output> 238 </output>
260 </test> 239 </test>
240 <test>
241 <conditional name="cm_opts">
242 <param name="cm_opts_selector" value="db"/>
243 <param name="database" value="minifam.cm" />
244 </conditional>
245 <param name="aux_files" value="minifam.tar" ftype="tar"/>
246 <param name="seqdb" value="metag-example.fa"/>
247 <output name="outfile" file="test_cmscan.tabular" ftype="tabular" lines_diff="8">
248 <assert_contents>
249 <has_n_lines n="15"/>
250 <has_text text="AAGA01015927.1"/>
251 </assert_contents>
252 </output>
253 </test>
261 254
262 </tests> 255 </tests>
263 <help> 256 <help>
264 <![CDATA[ 257 <![CDATA[
265 258