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

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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
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1 <?xml version="1.0"?>
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2 <tool id="kraken-mpa-report" name="Kraken-mpa-report" version="@WRAPPER_VERSION@">
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3 <description>view report of classification for multiple samples</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="version_command" />
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9 <command detect_errors="exit_code"><![CDATA[
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10 #set $names = []
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12 #for $input_count, $input_classification in enumerate( $classification ):
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13 #set $name_base = str( getattr( $input_classification, 'element_identifier', 'sample' ) ).replace( "/", '-' ).replace( "\t", "-" )
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14 #set $name = $name_base
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15 #set $i = 1
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16 #while $name in $names:
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17 #set $name = "%s_%s" % ( $name_base, $i )
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18 #set $i = $i + 1
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19 #end while
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20 #silent $names.append( $name )
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21 ln -s '${input_classification}' '${name}' &&
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22 #end for
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23
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24 @SET_DATABASE_PATH@ &&
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26 kraken-mpa-report
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27 @INPUT_DATABASE@
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28 #for $name in $names:
a3a7440fc618 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken_report/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
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29 "${name}"
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30 #end for
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32 ${show_zeros}
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33 ${header_line}
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34
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35 > '$output_report'
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36 ]]></command>
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37 <inputs>
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38 <param name="classification" format="tabular" label="Kraken output" multiple="True" type="data" />
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39 <param name="show_zeros" argument="--show-zeros" type="boolean" falsevalue="" truevalue="--show-zeros" checked="False"
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40 label="Display taxa even if they lack a read in any sample" />
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41 <param name="header_line" argument="--header-line" type="boolean" truevalue="--header-line" falsevalue="" checked="False"
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42 label="Display a header line indicating sample IDs"/>
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43
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44 <expand macro="input_database" />
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45 </inputs>
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46 <outputs>
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47 <data format="tabular" name="output_report" />
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48 </outputs>
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49 <tests>
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50 <test>
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51 <param name="classification" value="kraken_mpa_report_input1.tab,kraken_mpa_report_input2.tab" ftype="tabular"/>
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52 <param name="show_zeros" value="--show-zeros"/>
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53 <param name="header_line" value="--header-line"/>
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54 <param name="kraken_database" value="test_db"/>
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56 <output name="output_report" ftype="tabular" file="kraken_mpa_report_test1_output.tab" />
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57 </test>
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58 </tests>
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59 <help>
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60 <![CDATA[
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62 .. class:: warningmark
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64 **Note**: the database used must be the same as the one used in the original Kraken run
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66 -----
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68 **What is Does**
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69
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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.
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72 -----
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74 **Output**
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76 The output of kraken-mpa-report is a tab-delimited table, with one line per taxon.
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78 ]]>
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79 </help>
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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80 <expand macro="citations" />
f2757ab26483 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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81 </tool>