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bernt-matthiasbernt-matthias
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kraken2: remove unpaired paired input
1 parent 97fbd01 commit 451cf5e

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+28
-54
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2 files changed

+28
-54
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‎tool_collections/kraken2/kraken2/.lint_skip

Lines changed: 0 additions & 2 deletions
This file was deleted.

‎tool_collections/kraken2/kraken2/kraken2.xml

Lines changed: 28 additions & 52 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
<?xml version="1.0"?>
2-
<tool id="kraken2" name="Kraken2" version="@TOOL_VERSION@+galaxy1">
2+
<tool id="kraken2" name="Kraken2" version="@TOOL_VERSION@+galaxy2">
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<description>
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assign taxonomic labels to sequencing reads
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</description>
@@ -40,10 +40,7 @@
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$quick
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43-
#if $single_paired.single_paired_selector == "yes"
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--paired
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'${single_paired.forward_input}' '${single_paired.reverse_input}'
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#elif $single_paired.single_paired_selector == "collection":
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#if $single_paired.single_paired_selector == "collection":
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--paired
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'${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}'
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#else:
@@ -80,17 +77,12 @@
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<inputs>
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<conditional name="single_paired">
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<param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
83-
<option value="collection">Paired Collection</option>
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<option value="yes">Paired</option>
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<option value="collection">Paired</option>
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<option selected="True" value="no">Single</option>
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</param>
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<when value="collection">
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<param format="@INTYPES@" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads"/>
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</when>
90-
<when value="yes">
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<param format="@INTYPES@" name="forward_input" type="data" label="Forward strand"/>
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<param format="@INTYPES@" name="reverse_input" type="data" label="Reverse strand"/>
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</when>
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<when value="no">
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<param format="@INTYPES@" label="Input sequences" name="input_sequences" type="data"/>
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</when>
@@ -122,19 +114,6 @@
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<filter>(report['create_report'])</filter>
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</data>
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125-
<data name="out1" format_source="forward_input" label="${tool.name} on ${on_string}: Unclassified forward reads" from_work_dir="un_out_1.*">
126-
<filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter>
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</data>
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<data name="out2" format_source="forward_input" label="${tool.name} on ${on_string}: Unclassified reverse reads" from_work_dir="un_out_2.*">
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<filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter>
130-
</data>
131-
<data name="out3" format_source="forward_input" label="${tool.name} on ${on_string}: Classified forward reads" from_work_dir="cl_out_1.*">
132-
<filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter>
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</data>
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<data name="out4" format_source="forward_input" label="${tool.name} on ${on_string}: Classified reverse reads" from_work_dir="cl_out_2.*">
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<filter>(split_reads and ("yes" in single_paired['single_paired_selector']))</filter>
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</data>
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<collection name="out_unclassified_paired" type="paired" format_source="input_pair" label="${tool.name} on ${on_string}: Unclassified read pairs">
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<data name="forward" from_work_dir="un_out_1.*"/>
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<data name="reverse" from_work_dir="un_out_2.*"/>
@@ -151,37 +130,27 @@
151130
</outputs>
152131
<tests>
153132
<test expect_num_outputs="1">
154-
<param name="single_paired_selector" value="no"/>
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<param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/>
133+
<conditional name="single_paired">
134+
<param name="single_paired_selector" value="no"/>
135+
<param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/>
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</conditional>
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<param name="split_reads" value="false"/>
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<param name="quick" value="no"/>
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<param name="confidence" value=".2"/>
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<param name="kraken2_database" value="test_entry"/>
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<output name="output" file="kraken_test1_output.tab" ftype="tabular"/>
161142
</test>
162-
<test expect_num_outputs="5">
163-
<param name="single_paired_selector" value="yes"/>
164-
<param name="forward_input" value="kraken_test2_R1.fastq" ftype="fastq"/>
165-
<param name="reverse_input" value="kraken_test2_R2.fastq" ftype="fastq"/>
166-
<param name="split_reads" value="true"/>
167-
<param name="quick" value="no"/>
168-
<param name="confidence" value="0"/>
169-
<param name="kraken2_database" value="test_entry"/>
170-
<output name="out1" file="un_test2_output_1.fastq" ftype="fastq"/>
171-
<output name="out2" file="un_test2_output_2.fastq" ftype="fastq"/>
172-
<output name="out3" file="cl_test2_output_1.fastq" ftype="fastq"/>
173-
<output name="out4" file="cl_test2_output_2.fastq" ftype="fastq"/>
174-
<output name="output" file="kraken_test2_output.tab" ftype="tabular"/>
175-
</test>
176-
<!-- same test but collection in/output -->
177143
<test expect_num_outputs="7">
178-
<param name="single_paired_selector" value="collection"/>
179-
<param name="input_pair">
180-
<collection type="paired">
181-
<element name="forward" value="kraken_test2_R1.fastq" ftype="fastq"/>
182-
<element name="reverse" value="kraken_test2_R2.fastq" ftype="fastq"/>
183-
</collection>
184-
</param>
144+
<conditional name="single_paired">
145+
<param name="single_paired_selector" value="collection"/>
146+
<param name="input_pair">
147+
<collection type="paired">
148+
<element name="forward" value="kraken_test2_R1.fastq" ftype="fastq"/>
149+
<element name="reverse" value="kraken_test2_R2.fastq" ftype="fastq"/>
150+
</collection>
151+
</param>
152+
<param name="single_paired_selector" value="collection"/>
153+
</conditional>
185154
<param name="split_reads" value="true"/>
186155
<param name="quick" value="no"/>
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<param name="confidence" value="0"/>
@@ -196,11 +165,18 @@
196165
</output_collection>
197166
<output name="output" file="kraken_test2_output.tab" ftype="tabular"/>
198167
</test>
168+
199169
<test expect_num_outputs="2">
200-
<param name="single_paired_selector" value="yes"/>
201-
<param name="forward_input" value="kraken_test2_R1.fastq" ftype="fastq"/>
202-
<param name="reverse_input" value="kraken_test2_R2.fastq" ftype="fastq"/>
203-
<param name="use-names" value="true"/>
170+
<conditional name="single_paired">
171+
<param name="single_paired_selector" value="collection"/>
172+
<param name="input_pair">
173+
<collection type="paired">
174+
<element name="forward" value="kraken_test2_R1.fastq" ftype="fastq"/>
175+
<element name="reverse" value="kraken_test2_R2.fastq" ftype="fastq"/>
176+
</collection>
177+
</param>
178+
</conditional>
179+
<param name="use_names" value="true"/>
204180
<section name="report">
205181
<param name="create_report" value="true"/>
206182
<param name="report_minimizer_data" value="true"/>

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