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gatk_indel.xml
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gatk_indel.xml
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<tool id="gatk_indel" name="GATK INDEL" version="1.0.0">
<description>INDEL realignment</description>
<requirements>
<container type="docker">gatk</container>
</requirements>
<command interpreter="python">indel_realign.py
#if int($input.input_count) >= 1:
--input_file ${input.input_bam_1}
--input_file:index ${input.input_bam_1.metadata.bam_index}
#end if
#if int($input.input_count) >= 2:
--input_file ${input.input_bam_2}
--input_file:index ${input.input_bam_2.metadata.bam_index}
#end if
#if int($input.input_count) >= 3:
--input_file ${input.input_bam_3}
--input_file:index ${input.input_bam_3.metadata.bam_index}
#end if
#if int($input.input_count) >= 4:
--input_file ${input.input_bam_4}
--input_file:index ${input.input_bam_4.metadata.bam_index}
#end if
#if int($input.input_count) >= 5:
--input_file ${input.input_bam_5}
--input_file:index ${input.input_bam_5.metadata.bam_index}
#end if
#if int($input.input_count) >= 6:
--input_file ${input.input_bam_6}
--input_file:index ${input.input_bam_6.metadata.bam_index}
#end if
#if int($input.input_count) >= 7:
--input_file ${input.input_bam_7}
--input_file:index ${input.input_bam_7.metadata.bam_index}
#end if
#if int($input.input_count) >= 8:
--input_file ${input.input_bam_8}
--input_file:index ${input.input_bam_8.metadata.bam_index}
#end if
#if int($input.input_count) >= 9:
--input_file ${input.input_bam_9}
--input_file:index ${input.input_bam_9.metadata.bam_index}
#end if
#if int($input.input_count) >= 10:
--input_file ${input.input_bam_10}
--input_file:index ${input.input_bam_10.metadata.bam_index}
#end if
--reference-sequence ${reference}
--ncpus \${GALAXY_SLOTS:-8}
--workdir ./
#for $k in $known:
--known ${k.input}
#end for
#if int($input.input_count) >= 1:
--out output_1.bam
#end if
#if int($input.input_count) >= 2:
--out output_2.bam
#end if
#if int($input.input_count) >= 3:
--out output_3.bam
#end if
#if int($input.input_count) >= 4:
--out output_4.bam
#end if
#if int($input.input_count) >= 5:
--out output_5.bam
#end if
#if int($input.input_count) >= 6:
--out output_6.bam
#end if
#if int($input.input_count) >= 7:
--out output_7.bam
#end if
#if int($input.input_count) >= 8:
--out output_8.bam
#end if
#if int($input.input_count) >= 9:
--out output_9.bam
#end if
#if int($input.input_count) >= 10:
--out output_10.bam
#end if
--parallel-realign
--mem 16
</command>
<inputs>
<conditional name="input">
<param name="input_count" type="select" label="BAM Count">
<option value="1">1</option>
<option value="2">2</option>
<option value="3">3</option>
<option value="4">4</option>
<option value="5">5</option>
<option value="6">6</option>
<option value="7">7</option>
<option value="8">8</option>
<option value="9">9</option>
<option value="10">10</option>
</param>
<when value="1">
<param format="bam" type="data" name="input_bam_1" label="Input BAM 1" help="" />
</when>
<when value="2">
<param format="bam" type="data" name="input_bam_1" label="Input BAM 1" help="" />
<param format="bam" type="data" name="input_bam_2" label="Input BAM 2" help="" />
</when>
<when value="3">
<param format="bam" type="data" name="input_bam_1" label="Input BAM 1" help="" />
<param format="bam" type="data" name="input_bam_2" label="Input BAM 2" help="" />
<param format="bam" type="data" name="input_bam_3" label="Input BAM 3" help="" />
</when>
<when value="4">
<param format="bam" type="data" name="input_bam_1" label="Input BAM 1" help="" />
<param format="bam" type="data" name="input_bam_2" label="Input BAM 2" help="" />
<param format="bam" type="data" name="input_bam_3" label="Input BAM 3" help="" />
<param format="bam" type="data" name="input_bam_4" label="Input BAM 4" help="" />
</when>
<when value="5">
<param format="bam" type="data" name="input_bam_1" label="Input BAM 1" help="" />
<param format="bam" type="data" name="input_bam_2" label="Input BAM 2" help="" />
<param format="bam" type="data" name="input_bam_3" label="Input BAM 3" help="" />
<param format="bam" type="data" name="input_bam_4" label="Input BAM 4" help="" />
<param format="bam" type="data" name="input_bam_5" label="Input BAM 5" help="" />
</when>
<when value="6">
<param format="bam" type="data" name="input_bam_1" label="Input BAM 1" help="" />
<param format="bam" type="data" name="input_bam_2" label="Input BAM 2" help="" />
<param format="bam" type="data" name="input_bam_3" label="Input BAM 3" help="" />
<param format="bam" type="data" name="input_bam_4" label="Input BAM 4" help="" />
<param format="bam" type="data" name="input_bam_5" label="Input BAM 5" help="" />
<param format="bam" type="data" name="input_bam_6" label="Input BAM 6" help="" />
</when>
<when value="7">
<param format="bam" type="data" name="input_bam_1" label="Input BAM 1" help="" />
<param format="bam" type="data" name="input_bam_2" label="Input BAM 2" help="" />
<param format="bam" type="data" name="input_bam_3" label="Input BAM 3" help="" />
<param format="bam" type="data" name="input_bam_4" label="Input BAM 4" help="" />
<param format="bam" type="data" name="input_bam_5" label="Input BAM 5" help="" />
<param format="bam" type="data" name="input_bam_6" label="Input BAM 6" help="" />
<param format="bam" type="data" name="input_bam_7" label="Input BAM 7" help="" />
</when>
<when value="8">
<param format="bam" type="data" name="input_bam_1" label="Input BAM 1" help="" />
<param format="bam" type="data" name="input_bam_2" label="Input BAM 2" help="" />
<param format="bam" type="data" name="input_bam_3" label="Input BAM 3" help="" />
<param format="bam" type="data" name="input_bam_4" label="Input BAM 4" help="" />
<param format="bam" type="data" name="input_bam_5" label="Input BAM 5" help="" />
<param format="bam" type="data" name="input_bam_6" label="Input BAM 6" help="" />
<param format="bam" type="data" name="input_bam_7" label="Input BAM 7" help="" />
<param format="bam" type="data" name="input_bam_8" label="Input BAM 8" help="" />
</when>
<when value="9">
<param format="bam" type="data" name="input_bam_1" label="Input BAM 1" help="" />
<param format="bam" type="data" name="input_bam_2" label="Input BAM 2" help="" />
<param format="bam" type="data" name="input_bam_3" label="Input BAM 3" help="" />
<param format="bam" type="data" name="input_bam_4" label="Input BAM 4" help="" />
<param format="bam" type="data" name="input_bam_5" label="Input BAM 5" help="" />
<param format="bam" type="data" name="input_bam_6" label="Input BAM 6" help="" />
<param format="bam" type="data" name="input_bam_7" label="Input BAM 7" help="" />
<param format="bam" type="data" name="input_bam_8" label="Input BAM 8" help="" />
<param format="bam" type="data" name="input_bam_9" label="Input BAM 9" help="" />
</when>
<when value="10">
<param format="bam" type="data" name="input_bam_1" label="Input BAM 1" help="" />
<param format="bam" type="data" name="input_bam_2" label="Input BAM 2" help="" />
<param format="bam" type="data" name="input_bam_3" label="Input BAM 3" help="" />
<param format="bam" type="data" name="input_bam_4" label="Input BAM 4" help="" />
<param format="bam" type="data" name="input_bam_5" label="Input BAM 5" help="" />
<param format="bam" type="data" name="input_bam_6" label="Input BAM 6" help="" />
<param format="bam" type="data" name="input_bam_7" label="Input BAM 7" help="" />
<param format="bam" type="data" name="input_bam_8" label="Input BAM 8" help="" />
<param format="bam" type="data" name="input_bam_9" label="Input BAM 9" help="" />
<param format="bam" type="data" name="input_bam_10" label="Input BAM 10" help="" />
</when>
</conditional>
<param format="fasta" type="data" name="reference" label="Reference Genome" />
<repeat name="known" title="Known Variants">
<param name="input" type="data" format="vcf" label="Known Variant VCFs"/>
</repeat>
</inputs>
<outputs>
<data format="bam" name="output_bam_1" label="INDEL Realigned BAM 1" from_work_dir="output_1.bam">
<filter>int(input['input_count']) >= 1</filter>
</data>
<data format="bam" name="output_bam_2" label="INDEL Realigned BAM 2" from_work_dir="output_2.bam">
<filter>int(input['input_count']) >= 2</filter>
</data>
<data format="bam" name="output_bam_3" label="INDEL Realigned BAM 3" from_work_dir="output_3.bam">
<filter>int(input['input_count']) >= 3</filter>
</data>
<data format="bam" name="output_bam_4" label="INDEL Realigned BAM 4" from_work_dir="output_4.bam">
<filter>int(input['input_count']) >= 4</filter>
</data>
<data format="bam" name="output_bam_5" label="INDEL Realigned BAM 5" from_work_dir="output_5.bam">
<filter>int(input['input_count']) >= 5</filter>
</data>
<data format="bam" name="output_bam_6" label="INDEL Realigned BAM 6" from_work_dir="output_6.bam">
<filter>int(input['input_count']) >= 6</filter>
</data>
<data format="bam" name="output_bam_7" label="INDEL Realigned BAM 7" from_work_dir="output_7.bam">
<filter>int(input['input_count']) >= 7</filter>
</data>
<data format="bam" name="output_bam_8" label="INDEL Realigned BAM 8" from_work_dir="output_8.bam">
<filter>int(input['input_count']) >= 8</filter>
</data>
<data format="bam" name="output_bam_9" label="INDEL Realigned BAM 9" from_work_dir="output_9.bam">
<filter>int(input['input_count']) >= 9</filter>
</data>
<data format="bam" name="output_bam_10" label="INDEL Realigned BAM 10" from_work_dir="output_10.bam">
<filter>int(input['input_count']) >= 10</filter>
</data>
</outputs>
<stdio>
<exit_code range="1:" level="fatal" />
<regex match="ERROR"
source="both"
level="fatal"
description="Error running INDEL Realignment" />
</stdio>
<help>
</help>
<tests>
<test>
</test>
</tests>
</tool>