Mercurial > repos > devteam > kraken_report

comparison kraken-mpa-report.xml @ 4:a3a7440fc618 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken_report/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
author iuc
date Mon, 07 Aug 2017 17:29:32 -0400
parents 9ae975c30dde
children 6c09bed3444f
comparison
equal deleted inserted replaced
3:9ae975c30dde 4:a3a7440fc618
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="kraken-mpa-report" name="Kraken-mpa-report" version="1.2.1"> 2 <tool id="kraken-mpa-report" name="Kraken-mpa-report" version="@WRAPPER_VERSION@">
3 <description>view report of classification for multiple samples</description> 3 <description>view report of classification for multiple samples</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version_command" /> 8 <expand macro="version_command" />
10 <command> 9 <command detect_errors="exit_code"><![CDATA[
11 <![CDATA[ 10 #set $names = []
12 11
13 #for $input_count, $input_classification in enumerate( $classification ): 12 #for $input_count, $input_classification in enumerate( $classification ):
14 ln -s "${input_classification}" "sample_${input_count}" && 13 #set $name_base = str( getattr( $input_classification, 'element_identifier', 'sample' ) ).replace( "/", '-' ).replace( "\t", "-" )
15 #end for 14 #set $name = $name_base
15 #set $i = 1
16 #while $name in $names:
17 #set $name = "%s_%s" % ( $name_base, $i )
18 #set $i = $i + 1
19 #end while
20 #silent $names.append( $name )
21 ln -s '${input_classification}' '${name}' &&
22 #end for
16 23
17 @SET_DATABASE_PATH@ && kraken-mpa-report @INPUT_DATABASE@ 24 @SET_DATABASE_PATH@ &&
18 25
19 #for $input_count, $input_classification in enumerate( $classification ): 26 kraken-mpa-report
20 "sample_${input_count}" 27 @INPUT_DATABASE@
21 #end for 28 #for $name in $names:
29 "${name}"
30 #end for
22 31
23 ${show_zeros} 32 ${show_zeros}
24 ${header_line} 33 ${header_line}
25 34
26 > "$output_report" 35 > '$output_report'
27 ]]> 36 ]]></command>
28 </command>
29 <inputs> 37 <inputs>
30 <param format="tabular" label="Kraken output" multiple="True" name="classification" type="data" /> 38 <param name="classification" format="tabular" label="Kraken output" multiple="True" type="data" />
31 <param checked="False" falsevalue="" help="--show-zeros" label="Display taxa even if they lack a read in any sample" name="show_zeros" truevalue="--show-zeros" type="boolean" /> 39 <param name="show_zeros" argument="--show-zeros" type="boolean" falsevalue="" truevalue="--show-zeros" checked="False"
32 <param checked="False" falsevalue="" help="--header-line" label="Display a header line indicating sample IDs" name="header_line" truevalue="--header-line" type="boolean" /> 40 label="Display taxa even if they lack a read in any sample" />
41 <param name="header_line" argument="--header-line" type="boolean" truevalue="--header-line" falsevalue="" checked="False"
42 label="Display a header line indicating sample IDs"/>
43
33 <expand macro="input_database" /> 44 <expand macro="input_database" />
34 </inputs> 45 </inputs>
35 <outputs> 46 <outputs>
36 <data format="tabular" name="output_report" /> 47 <data format="tabular" name="output_report" />
37 </outputs> 48 </outputs>
39 <test> 50 <test>
40 <param name="classification" value="kraken_mpa_report_input1.tab,kraken_mpa_report_input2.tab" ftype="tabular"/> 51 <param name="classification" value="kraken_mpa_report_input1.tab,kraken_mpa_report_input2.tab" ftype="tabular"/>
41 <param name="show_zeros" value="--show-zeros"/> 52 <param name="show_zeros" value="--show-zeros"/>
42 <param name="header_line" value="--header-line"/> 53 <param name="header_line" value="--header-line"/>
43 <param name="kraken_database" value="test_db"/> 54 <param name="kraken_database" value="test_db"/>
44 <output name="output_report" file="kraken_mpa_report_test1_output.tab" ftype="tabular"/> 55
56 <output name="output_report" ftype="tabular" file="kraken_mpa_report_test1_output.tab" />
45 </test> 57 </test>
46 </tests> 58 </tests>
47 <help> 59 <help>
48 <![CDATA[ 60 <![CDATA[
49 61
53 65
54 ----- 66 -----
55 67
56 **What is Does** 68 **What is Does**
57 69
58 Kraken-mpa-report summarizes read counts across taxonomic ranks for multiple samples. This is convenient for comparing results across multiple expreriments, conditions, locations, etc. It support sthe following parameters:: 70 Kraken-mpa-report summarizes read counts across taxonomic ranks for multiple samples. This is convenient for comparing results across multiple experiments, conditions, locations, etc.
59
60 --show-zeros Display taxa even if they lack a read in any sample
61 --header-line Display a header line indicating sample IDs
62 (sample IDs are the filenames)
63 71
64 ----- 72 -----
65 73
66 **Output** 74 **Output**
67 75
68 The output of kraken-mpa-report is tab-delimited, with one line per taxon. 76 The output of kraken-mpa-report is a tab-delimited table, with one line per taxon.
69 77
70 ]]> 78 ]]>
71 </help> 79 </help>
72 <expand macro="citations" /> 80 <expand macro="citations" />
73 </tool> 81 </tool>