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Updated tool xml outputs format and bumped galaxy version. #12

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Updated tool xml outputs format and bumped galaxy version. #12

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3b53b1a
Updated tool xml outputs format and bumped galaxy version.
thobalose Mar 25, 2019
3257b89
Merge branch 'master' of github.com:COMBAT-TB/confil into dev
thobalose Mar 25, 2019
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25 changes: 13 additions & 12 deletions confil.xml
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Original file line number Diff line number Diff line change
@@ -1,12 +1,13 @@
<tool id="confil" name="Contamination Filter (confil)" version="@VERSION@+galaxy0">
<tool id="confil" name="Contamination Filter (confil)" version="@VERSION@+galaxy1">
<macros>
<token name="@VERSION@">0.1.5</token>
</macros>
<requirements>
<requirement type="package" version="@VERSION@">confil</requirement>
<requirement type="package" version="7.0">click</requirement>
</requirements>
<command detect_errors="exit_code"><![CDATA[
<command detect_errors="exit_code">
<![CDATA[
#set $input_type = $input_type_conditional.input_type
#import re

Expand Down Expand Up @@ -61,13 +62,13 @@
</inputs>
<outputs>
<data name="output_report" format="tabular" label="${tool.name} on ${on_string} kraken2 report" />
<data name="single_output_file" format="fastq" label="${tool.name} on ${on_string} single output">
<data name="single_output_file" format_source="single_input" metadata_source="single_input" label="${tool.name} on ${on_string} single output">
<filter>input_type_conditional['input_type'] == "single"</filter>
</data>
<collection name="list_output" type="paired" label="${tool.name} on ${on_string} paired output" structured_like="collection_input" inherit_format="true">
<filter>input_type_conditional['input_type'] == "paired_collection"</filter>
<data name="forward" format="fastq" />
<data name="reverse" format="fastq" />
<data name="forward" format_source="${collection_input.forward}" metadata_source="${collection_input.forward}" />
<data name="reverse" format_source="${collection_input.reverse}" metadata_source="${collection_input.reverse}" />
</collection>
</outputs>
<tests>
Expand All @@ -85,18 +86,18 @@
</collection>
</param>
<param name="input_type" value="paired_collection" />
<output name="output_report" ftype='tabular' file="seq.tab" />
<output name="output_report" ftype="tabular" file="seq.tab" />
<output_collection name="list_output" type="paired">
<element name="forward" value="seq_1.fastq">
</element>
<element name="reverse" value="seq_2.fastq">
</element>
<element name="forward" value="seq_1.fastq"></element>
<element name="reverse" value="seq_2.fastq"></element>
</output_collection>
</test>
</tests>
<help><![CDATA[
<help>
<![CDATA[
confil parses a kraken2 report and determines contamination based on a specified cutoff.
]]> </help>
]]>
</help>
<citations>
<citation type="bibtex">
@misc{githubconfil,
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