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Add requirements to all converters that use bgzip.py

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This commit is contained in:
mvdbeek
2020-02-09 16:44:20 +01:00
parent 6ebb796c56
commit 21a0324887
6 changed files with 30 additions and 6 deletions
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lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml
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<tool id="CONVERTER_bed_to_bgzip_0" name="Convert BED to BGZIP" version="1.0.0" hidden="true">
<tool id="CONVERTER_bed_to_bgzip_0" name="Convert BED to BGZIP" version="1.0.1" hidden="true" profile="16.04">
<!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
<requirements>
<requirement type="package" version="0.15.4">pysam</requirement>
<requirement type="package" version="8.25">coreutils</requirement>
</requirements>
<command>python '$__tool_directory__/bgzip.py' -P bed '$input1' '$output1'</command>
<inputs>
<param format="bed" name="input1" type="data" label="Choose BED file"/>
lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml
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<tool id="CONVERTER_encodepeak_to_bgzip_0" name="Convert ENCODEPeak to BGZIP" version="1.0.0" hidden="true">
<tool id="CONVERTER_encodepeak_to_bgzip_0" name="Convert ENCODEPeak to BGZIP" version="1.0.1" hidden="true" profile="16.04">
<!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
<requirements>
<requirement type="package" version="0.15.4">pysam</requirement>
<requirement type="package" version="8.25">coreutils</requirement>
</requirements>
<command>
python '$__tool_directory__/bgzip.py'
-c ${input1.metadata.chromCol}
lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml
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<tool id="CONVERTER_gff_to_bgzip_0" name="Convert GFF to BGZIP" version="1.0.0" hidden="true">
<tool id="CONVERTER_gff_to_bgzip_0" name="Convert GFF to BGZIP" version="1.0.1" hidden="true" profile="16.04">
<!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
<requirements>
<requirement type="package" version="0.15.4">pysam</requirement>
<requirement type="package" version="8.25">coreutils</requirement>
</requirements>
<command>python '$__tool_directory__/bgzip.py' -P gff '$input1' '$output1'</command>
<inputs>
<param format="gff" name="input1" type="data" label="Choose GFF file"/>
lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
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<tool id="CONVERTER_interval_to_bgzip_0" name="Convert Interval to BGZIP" version="1.0.0" hidden="true">
<tool id="CONVERTER_interval_to_bgzip_0" name="Convert Interval to BGZIP" version="1.0.1" hidden="true" profile="16.04">
<!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
<requirements>
<requirement type="package" version="0.15.4">pysam</requirement>
<requirement type="package" version="8.25">coreutils</requirement>
</requirements>
<command>
python '$__tool_directory__/bgzip.py'
-c ${input1.metadata.chromCol}
lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml
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<tool id="CONVERTER_vcf_to_bgzip_0" name="Convert VCF to BGZIP" version="1.0.0" hidden="true">
<tool id="CONVERTER_vcf_to_bgzip_0" name="Convert VCF to BGZIP" version="1.0.1" hidden="true" profile="16.04">
<!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
<requirements>
<requirement type="package" version="0.15.4">pysam</requirement>
<requirement type="package" version="8.25">coreutils</requirement>
</requirements>
<command>python '$__tool_directory__/bgzip.py' -P vcf '$input1' '$output1'</command>
<inputs>
<param format="vcf" name="input1" type="data" label="Choose Vcf file"/>
lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml
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<tool id="CONVERTER_vcf_to_vcf_bgzip_0" name="Convert VCF to VCF_BGZIP" version="1.0.1" hidden="true">
<tool id="CONVERTER_vcf_to_vcf_bgzip_0" name="Convert VCF to VCF_BGZIP" version="1.0.2" hidden="true" profile="16.04">
<!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
<requirements>
<requirement type="package" version="0.15.4">pysam</requirement>
<requirement type="package" version="8.25">coreutils</requirement>
</requirements>
<command>python '$__tool_directory__/vcf_to_vcf_bgzip.py' '$input1' '$output1'</command>
<inputs>
<param format="vcf" name="input1" type="data" label="Choose Vcf file"/>