diff kraken-mpa-report.xml @ 9:8ddbdc9cdc57 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 1590e274eaa41ea77a6017111f9122e0a58aa75d-dirty"

--- a/kraken-mpa-report.xml	Thu Sep 13 09:44:00 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,81 +0,0 @@
-<?xml version="1.0"?>
-<tool id="kraken-mpa-report" name="Kraken-mpa-report" version="@WRAPPER_VERSION@">
-    <description>view report of classification for multiple samples</description>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements" />
-    <expand macro="version_command" />
-    <command detect_errors="exit_code"><![CDATA[
-    #set $names = []
-
-    #for $input_count, $input_classification in enumerate( $classification ):
-        #set $name_base = str( getattr( $input_classification, 'element_identifier', 'sample' ) ).replace( "/", '-' ).replace( "\t", "-" )
-        #set $name = $name_base
-        #set $i = 1
-        #while $name in $names:
-            #set $name = "%s_%s" % ( $name_base, $i )
-            #set $i = $i + 1
-        #end while
-        #silent $names.append( $name )
-        ln -s '${input_classification}' '${name}' &&
-    #end for
-
-    @SET_DATABASE_PATH@ &&
-
-    kraken-mpa-report
-        @INPUT_DATABASE@
-        #for $name in $names:
-            '${name}'
-        #end for
-
-        ${show_zeros}
-        ${header_line}
-
-        > '$output_report'
-    ]]></command>
-    <inputs>
-        <param name="classification" format="tabular" label="Kraken output" multiple="True" type="data" />
-        <param name="show_zeros" argument="--show-zeros" type="boolean" falsevalue=""  truevalue="--show-zeros" checked="False"
-               label="Display taxa even if they lack a read in any sample" />
-        <param name="header_line" argument="--header-line" type="boolean" truevalue="--header-line" falsevalue="" checked="False"
-               label="Display a header line indicating sample IDs"/>
-
-        <expand macro="input_database" />
-    </inputs>
-    <outputs>
-        <data format="tabular" name="output_report" />
-    </outputs>
-    <tests>
-        <test>
-            <param name="classification" value="kraken_mpa_report_input1.tab,kraken_mpa_report_input2.tab" ftype="tabular"/>
-            <param name="show_zeros" value="--show-zeros"/>
-            <param name="header_line" value="--header-line"/>
-            <param name="kraken_database" value="test_db"/>
-
-            <output name="output_report" ftype="tabular" file="kraken_mpa_report_test1_output.tab" />
-        </test>
-    </tests>
-    <help>
-<![CDATA[
-
-.. class:: warningmark
-
-**Note**: the database used must be the same as the one used in the original Kraken run
-
------
-
-**What is Does**
-
-Kraken-mpa-report summarizes read counts across taxonomic ranks for multiple samples. This is convenient for comparing results across multiple experiments, conditions, locations, etc.
-
------
-
-**Output**
-
-The output of kraken-mpa-report is a tab-delimited table, with one line per taxon.
-
-]]>
-    </help>
-    <expand macro="citations" />
-</tool>