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Add --local option to Bismark Bowtie2 Wrapper (continuation from PR #1537, part 2) #1545

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Add --local option to Bismark Bowtie2 Wrapper (continuation from PR #1537, part 2) #1545

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918a345
update requirement versions; handle lint warnings
jooner14 Oct 31, 2024
fdd2d09
Merge branch 'bgruening:master' into master
jonasbucherETH Nov 15, 2024
a0e1f18
Moved and updated bismark files to tools/bismark
jooner14 Nov 15, 2024
f91ffd6
remove unnecessary file
jooner14 Nov 15, 2024
5e20387
Delete .shed.yml
bgruening Nov 16, 2024
9a5a55b
fix tests, reformatting
bgruening Nov 16, 2024
38d0d32
update test data
bgruening Nov 16, 2024
521ba62
udpate version
bgruening Nov 16, 2024
fed06aa
update test data
bgruening Nov 16, 2024
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10 changes: 5 additions & 5 deletions tools/bismark/bismark2report_wrapper.xml
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
<tool id="bismark_pretty_report" name="Bismark Pretty Report" version="0.22.1" profile="17.01">
<tool id="bismark_pretty_report" name="Bismark Pretty Report" version="0.24.2+galaxy0" profile="22.01">
<description>Generates a graphical HTML report page from report outputs of Bismark</description>
<requirements>
<requirement type="package" version="0.22.1">bismark</requirement>
<requirement type="package" version="1.8">samtools</requirement>
<requirement type="package" version="2.3.5">bowtie2</requirement>
<requirement type="package" version="0.24.2">bismark</requirement>
<requirement type="package" version="1.21">samtools</requirement>
<requirement type="package" version="2.5.4">bowtie2</requirement>
</requirements>
<command><![CDATA[
python '$__tool_directory__/bismark2report_wrapper.py'
Expand Down Expand Up @@ -57,7 +57,7 @@
</outputs>

<tests>
<test>
<test expect_num_outputs="1">
<param name="alignment" value="mapping_report.txt" ftype="txt"/>
<param name="dedup" value="dedup_report.txt" ftype="txt"/>
<param name="splitting" value="output_splitting_report.txt" ftype="txt"/>
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33 changes: 20 additions & 13 deletions tools/bismark/bismark_bowtie2_wrapper.xml
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@@ -1,9 +1,9 @@
<tool id="bismark_bowtie2" name="Bismark Mapper" version="0.22.1+galaxy4" profile="18.01">
<tool id="bismark_bowtie2" name="Bismark Mapper" version="0.24.2+galaxy0" profile="22.01">
<description>Bisulfite reads mapper</description>
<requirements>
<requirement type="package" version="0.22.1">bismark</requirement>
<requirement type="package" version="1.8">samtools</requirement>
<requirement type="package" version="2.3.5">bowtie2</requirement>
<requirement type="package" version="0.24.2">bismark</requirement>
<requirement type="package" version="1.21">samtools</requirement>
<requirement type="package" version="2.5.4">bowtie2</requirement>
</requirements>
<command><![CDATA[
#import re
Expand Down Expand Up @@ -167,6 +167,8 @@

$params.pbat

$params.local

#if $params.bismark_stdout:
--stdout '$output_stdout'
#end if
Expand Down Expand Up @@ -296,7 +298,7 @@
<param name="skip_reads" type="integer" value="0"
label="Skip (i.e. do not align) the first N reads or read pairs from the input"/>

<param argument="--score-min" name="score_min" type="text" value="" label="Set a function governing the minimum alignment score needed for an alignment to be considered `valid` (i.e. good enough to report)" help="This is a function of read length. For instance, specifying `L,0,-0.2` sets the minimum-score function `f` to `f(x) = 0 + -0.2 * x`, where `x` is the read length."/>
<param argument="--score-min" type="text" value="" label="Set a function governing the minimum alignment score needed for an alignment to be considered `valid` (i.e. good enough to report)" help="This is a function of read length. For instance, specifying `L,0,-0.2` sets the minimum-score function `f` to `f(x) = 0 + -0.2 * x`, where `x` is the read length."/>

<param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="false"
label="Disable looking for discordant alignments if it cannot find any concordant alignments (only for paired-end reads)"
Expand All @@ -315,13 +317,17 @@
label="Write the bismark output and summary information to an extra file"/>
<param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="true"
label="Offer all report files concatenated in one file (Mapping Report)"/>
<param argument="--non_directional" name="non_directional" type="boolean"
<param argument="--non_directional" type="boolean"
truevalue="--non_directional" falsevalue="" checked="false"
label="The sequencing library was constructed in a non strand-specific manner, alignments to all four bisulfite strands will be reported."/>
<param argument="--pbat" name="pbat" type="boolean"
<param argument="--pbat" type="boolean"
truevalue="--pbat" falsevalue="" checked="false"
label="Treat input data as PBAT-Seq libraries"
help="Use this option only if you are certain that your libraries were constructed following a PBAT protocol. If you don't know what PBAT-Seq is you should not specify this option." />
<param argument="--local" type="boolean"
truevalue="--local" falsevalue="" checked="false"
label="Allow local alignments"
help="In this mode, it is not required that the entire read aligns from one end to the other. Rather, some characters may be omitted (“soft-clipped”) from the ends." />


<!--end output options -->
Expand Down Expand Up @@ -471,7 +477,7 @@
</data>
</outputs>
<tests>
<test>
<test expect_num_outputs="5">
<param name="genomeSource" value="history"/>
<param name="own_file" value="mm10.tiny.fa.gz" />
<param name="sPaired" value="single"/>
Expand All @@ -495,7 +501,7 @@
<output name="report_file" file="mapping_report.txt" ftype="txt" lines_diff="6"/>
<output name="output" file="mapped_reads.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
</test>
<test>
<test expect_num_outputs="5">
<param name="genomeSource" value="history"/>
<param name="own_file" value="mm10.tiny.fa.gz" />
<param name="sPaired" value="single"/>
Expand All @@ -519,7 +525,7 @@
<output name="report_file" file="mapping_report_short.txt" ftype="txt" lines_diff="6"/>
<output name="output" file="mapped_reads_short.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
</test>
<test>
<test expect_num_outputs="7">
<param name="genomeSource" value="history"/>
<param name="own_file" value="mm10.tiny.fa.gz" />
<param name="sPaired" value="paired"/>
Expand All @@ -546,7 +552,7 @@
<output name="report_file" file="mapping_report_mate.txt" ftype="txt" lines_diff="6"/>
<output name="output" file="mapped_reads_mate.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
</test>
<test>
<test expect_num_outputs="7">
<param name="genomeSource" value="history"/>
<param name="own_file" value="mm10.tiny.fa.gz" />
<param name="sPaired" value="paired"/>
Expand Down Expand Up @@ -577,7 +583,7 @@
<output name="report_file" file="mapping_report_mate_two_samples.txt" ftype="txt" lines_diff="12"/>
<output name="output" file="mapped_reads_mate_two_samples.bam" ftype="qname_input_sorted.bam" lines_diff="14"/>
</test>
<test>
<test expect_num_outputs="5">
<param name="genomeSource" value="history"/>
<param name="own_file" value="mm10.tiny.fa.gz" />
<param name="sPaired" value="single"/>
Expand Down Expand Up @@ -609,7 +615,7 @@
<has_text text="--score-min 'L,0,-0.8'" />
</assert_command>
</test>
<test>
<test expect_num_outputs="5">
<param name="genomeSource" value="history"/>
<param name="own_file" value="mm10.tiny.fa.gz" />
<param name="sPaired" value="single"/>
Expand Down Expand Up @@ -640,6 +646,7 @@
<assert_command>
<has_text text="--pbat" />
</assert_command>

</test>
</tests>

Expand Down
10 changes: 5 additions & 5 deletions tools/bismark/bismark_deduplicate_wrapper.xml
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
<tool id="bismark_deduplicate" name="Bismark Deduplicate" version="0.22.1" profile="18.01">
<tool id="bismark_deduplicate" name="Bismark Deduplicate" version="0.24.2+galaxy0" profile="22.01">
<description>Deduplicates reads mapped by Bismark</description>
<requirements>
<requirement type="package" version="0.22.1">bismark</requirement>
<requirement type="package" version="1.8">samtools</requirement>
<requirement type="package" version="2.3.5">bowtie2</requirement>
<requirement type="package" version="0.24.2">bismark</requirement>
<requirement type="package" version="1.21">samtools</requirement>
<requirement type="package" version="2.5.4">bowtie2</requirement>
</requirements>
<command><![CDATA[
python '$__tool_directory__/bismark_deduplicate_wrapper.py'
Expand Down Expand Up @@ -39,7 +39,7 @@
</outputs>

<tests>
<test>
<test expect_num_outputs="2">
<param name="sPaired" value="single"/>
<param name="mapping_output" value="mapped_reads.bam" ftype="qname_sorted.bam"/>
<output name="output_bam" file="dedup_reads.bam" ftype="qname_sorted.bam"/>
Expand Down
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