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Add bio.tools IDs to tool wrappers #616

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5b62f01
Add bio.tools ID to cd_hit_dup.xml
supernord Oct 31, 2023
ec34180
Add bio.tools ID to multispecies_MicrosatDataGenerator_interrupted_GA…
supernord Oct 31, 2023
4a467b9
Merge pull request #1 from supernord/patch-1
supernord Oct 31, 2023
446167a
Add bio.tools ID to quality_filter.xml
supernord Oct 31, 2023
112d355
Add bio.tools ID to gi2taxonomy.xml
supernord Oct 31, 2023
be8032c
Add bio.tools ID to kraken2tax.xml
supernord Oct 31, 2023
19257a9
Add bio.tools ID to lca.xml
supernord Nov 3, 2023
d85e973
Add bio.tools ID to t2ps_wrapper.xml
supernord Nov 3, 2023
9e05ed4
Add bio.tools ID to t2t_report.xml
supernord Nov 3, 2023
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3 changes: 3 additions & 0 deletions tool_collections/taxonomy/gi2taxonomy/gi2taxonomy.xml
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Expand Up @@ -3,6 +3,9 @@
<requirements>
<requirement type="package" version="1.0.0">taxonomy</requirement>
</requirements>
<xrefs>
<xref type="bio.tools">gi2taxonomy</xref>
</xrefs>
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I think this tool should be moved to deprecated instead, it doesn't seem to be installed on big 3 servers and its requirement is not installable any more (no conda package, sources on BitBucket removed).

<command interpreter="python">gi2taxonomy.py $input $giField $idField $out_file1 ${GALAXY_DATA_INDEX_DIR}</command>
<inputs>
<param format="tabular" name="input" type="data" label="Show taxonomic representation for"></param>
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3 changes: 3 additions & 0 deletions tool_collections/taxonomy/kraken2tax/kraken2tax.xml
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Expand Up @@ -4,6 +4,9 @@
<requirement type="package" version="5.1.0">gawk</requirement>
<requirement type="package" version="1.0.1">gb_taxonomy_tools</requirement>
</requirements>
<xrefs>
<xref type="bio.tools">kraken2tax</xref>
</xrefs>
<command>
<![CDATA[
awk '{ print \$${read_name}, \$${tax_id} }' OFS="\t" "${input}" | taxonomy-reader "${ncbi_taxonomy.fields.path}/names.dmp" "${ncbi_taxonomy.fields.path}/nodes.dmp" 1 > "${out_file}"
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5 changes: 4 additions & 1 deletion tools/cd_hit_dup/cd_hit_dup.xml
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Expand Up @@ -5,6 +5,9 @@
<requirements>
<requirement type="package" version="0.5-2012-03-07-fix-dan-gh-0.0.1">cd-hit-auxtools</requirement>
</requirements>
<xrefs>
<xref type="bio.tools">cd-hit</xref>
</xrefs>
<stdio>
<exit_code range="1:" />
<exit_code range=":-1" />
Expand Down Expand Up @@ -122,4 +125,4 @@ cd-hit-dup provides a number of options to tune how the duplicates are removed::
<citations>
<citation type="doi">10.1093/bioinformatics/bts565</citation>
</citations>
</tool>
</tool>
3 changes: 3 additions & 0 deletions ...tispecies_orthologous_microsats/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml
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@@ -1,5 +1,8 @@
<tool id="multispecies_orthologous_microsats" name="Extract orthologous microsatellites" version="1.0.0">
<description> for multiple (>2) species alignments</description>
<xrefs>
<xref type="bio.tools">multispecies_orthologous_microsats</xref>
</xrefs>
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This tool also should probably be moved to deprecated/.

<command interpreter="perl">
multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl
$input1
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3 changes: 3 additions & 0 deletions tools/quality_filter/quality_filter.xml
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Expand Up @@ -4,6 +4,9 @@
<requirement type="package" version="0.7.1">bx-python</requirement>
<requirement type="package" version="1.7.1">numpy</requirement>
</requirements>
<xrefs>
<xref type="bio.tools">qualityfilter</xref>
</xrefs>
<command interpreter="python">
quality_filter.py
$input
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