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<!-- same as mulled_example_multi_1, but requirements use builds | ||
used to show that this does not yield the same mulled v2 hash, | ||
i.e. the build is considered as part of version --> | ||
<tool id="mulled_example_multi_2" name="mulled_example_multi_2" version="0.1.0" license="AFL-3.0"> | ||
<xrefs> | ||
<xref type="bio.tools">bedtools</xref> | ||
<xref type="bio.tools">samtools</xref> | ||
</xrefs> | ||
<creator> | ||
<person | ||
givenName="Björn" | ||
familyName="Grüning" | ||
url="https://github.com/bgruening" | ||
identifier="http://orcid.org/0000-0002-3079-6586" /> | ||
<organization | ||
url="https://galaxyproject.org/iuc/" | ||
name="Galaxy IUC" /> | ||
</creator> | ||
<requirements> | ||
<requirement type="package" version="1.3.1=h9071d68_10">samtools</requirement> | ||
<requirement type="package" version="2.26.0=0">bedtools</requirement> | ||
</requirements> | ||
<command><![CDATA[ | ||
bedtools --version > '$out_file1' && | ||
echo "Moo" >> '$out_file1' && | ||
samtools >> '$out_file1' 2>&1 && | ||
echo "Cow" >> '$out_file1' && | ||
touch "\${TMP:-/tmp}/job_tmp" && | ||
touch "\${TEMP:-/tmp}/job_temp" && | ||
touch "\${TMPDIR:-/tmp}/job_tmpdir" | ||
]]></command> | ||
<inputs> | ||
<param name="input1" type="data" optional="true" /> | ||
</inputs> | ||
<outputs> | ||
<data name="out_file1" format="txt" /> | ||
</outputs> | ||
<tests> | ||
</tests> | ||
<help><![CDATA[ | ||
This is an example mulled tool that combines bedtools and samtools in one | ||
command-line invocation. | ||
]]></help> | ||
<citations> | ||
<citation type="doi">10.1093/bioinformatics/btq033</citation> | ||
<citation type="bibtex"> | ||
@misc{SAM_def, | ||
title={Definition of SAM/BAM format}, | ||
url = {https://samtools.github.io/hts-specs/},} | ||
</citation> | ||
<citation type="doi">10.1093/bioinformatics/btp352</citation> | ||
<citation type="doi">10.1093/bioinformatics/btr076</citation> | ||
<citation type="doi">10.1093/bioinformatics/btr509</citation> | ||
<citation type="bibtex"> | ||
@misc{Danecek_et_al, | ||
Author={Danecek, P., Schiffels, S., Durbin, R.}, | ||
title={Multiallelic calling model in bcftools (-m)}, | ||
url = {http://samtools.github.io/bcftools/call-m.pdf},} | ||
</citation> | ||
<citation type="bibtex"> | ||
@misc{Durbin_VCQC, | ||
Author={Durbin, R.}, | ||
title={Segregation based metric for variant call QC}, | ||
url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} | ||
</citation> | ||
<citation type="bibtex"> | ||
@misc{Li_SamMath, | ||
Author={Li, H.}, | ||
title={Mathematical Notes on SAMtools Algorithms}, | ||
url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} | ||
</citation> | ||
<citation type="bibtex"> | ||
@misc{SamTools_github, | ||
title={SAMTools GitHub page}, | ||
url = {https://github.com/samtools/samtools},} | ||
</citation> | ||
</citations> | ||
</tool> |