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Add bio.tools to wrappers #29

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May 17, 2024
Merged

Add bio.tools to wrappers #29

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4 changes: 3 additions & 1 deletion tools/frogs/affiliation_filters.xml
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<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements"/> <command detect_errors="exit_code">
<expand macro="xrefs"/>
<expand macro="requirements"/>
<command detect_errors="exit_code">
affiliation_filters.py
--input-biom '$input_biom'
--input-fasta '$input_fasta'
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1 change: 1 addition & 0 deletions tools/frogs/affiliation_postprocess.xml
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<macros>
<import>macros.xml</import>
</macros>
<expand macro="xrefs"/>
<expand macro="requirements"/>
<command detect_errors="exit_code">
affiliation_postprocess.py
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1 change: 1 addition & 0 deletions tools/frogs/affiliation_stats.xml
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<macros>
<import>macros.xml</import>
</macros>
<expand macro="xrefs"/>
<expand macro="requirements"/>
<command detect_errors="exit_code">
affiliation_stats.py
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1 change: 1 addition & 0 deletions tools/frogs/biom_to_stdBiom.xml
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<macros>
<import>macros.xml</import>
</macros>
<expand macro="xrefs"/>
<expand macro="requirements"/>
<command detect_errors="exit_code">
biom_to_stdBiom.py
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1 change: 1 addition & 0 deletions tools/frogs/biom_to_tsv.xml
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<macros>
<import>macros.xml</import>
</macros>
<expand macro="xrefs"/>
<expand macro="requirements"/>
<command detect_errors="exit_code">
biom_to_tsv.py
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2 changes: 1 addition & 1 deletion tools/frogs/cluster_filters.xml
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<macros>
<import>macros.xml</import>
</macros>

<expand macro="xrefs"/>
<expand macro="requirements">
<requirement type="package" version="2.10">blast</requirement>
</expand>
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1 change: 1 addition & 0 deletions tools/frogs/cluster_stats.xml
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<macros>
<import>macros.xml</import>
</macros>
<expand macro="xrefs"/>
<expand macro="requirements"/>
<command detect_errors="exit_code">
cluster_stats.py
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1 change: 1 addition & 0 deletions tools/frogs/clustering.xml
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<macros>
<import>macros.xml</import>
</macros>
<expand macro="xrefs"/>
<expand macro="requirements">
<requirement type="package" version="3.0.0">swarm</requirement>
</expand>
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1 change: 1 addition & 0 deletions tools/frogs/demultiplex.xml
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<macros>
<import>macros.xml</import>
</macros>
<expand macro="xrefs"/>
<expand macro="requirements" />
<command detect_errors="exit_code">
demultiplex.py
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1 change: 1 addition & 0 deletions tools/frogs/deseq2_preprocess.xml
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<macros>
<import>macros.xml</import>
</macros>
<expand macro="xrefs"/>
<expand macro="requirements_phyloseq">
<requirement type="package" version="1.34.0">bioconductor-deseq2</requirement>
<requirement type="package" version="1.6.6">r-optparse</requirement>
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1 change: 1 addition & 0 deletions tools/frogs/deseq2_visualisation.xml
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<macros>
<import>macros.xml</import>
</macros>
<expand macro="xrefs"/>
<expand macro="requirements_phyloseq">
<requirement type="package" version="1.34.0">bioconductor-deseq2</requirement>
<requirement type="package" version="0.18">r-dt</requirement>
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13 changes: 5 additions & 8 deletions tools/frogs/frogsfunc_functions.xml
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-->
<tool id="FROGSFUNC_step2_functions" name="FROGSFUNC_2_functions" version= "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
<description>Calculates functions abundances in each sample. </description>

<macros>
<import>macros.xml</import>
</macros>

<expand macro="requirements_frogsfunc" />


<macros>
<import>macros.xml</import>
</macros>
<expand macro="xrefs"/>
<expand macro="requirements_frogsfunc" />
<stdio>
<exit_code range="1:" />
<exit_code range=":-1" />
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1 change: 1 addition & 0 deletions tools/frogs/frogsfunc_pathways.xml
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<import>macros.xml</import>
</macros>

<expand macro="xrefs"/>
<expand macro="requirements_frogsfunc" />

<stdio>
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2 changes: 1 addition & 1 deletion tools/frogs/frogsfunc_placeseqs.xml
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<macros>
<import>macros.xml</import>
</macros>

<expand macro="xrefs"/>
<expand macro="requirements_frogsfunc" >
<requirement type="package" version="4.5.2">dendropy</requirement>
</expand>
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1 change: 1 addition & 0 deletions tools/frogs/itsx.xml
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<macros>
<import>macros.xml</import>
</macros>
<expand macro="xrefs"/>
<expand macro="requirements">
<requirement type="package" version="1.1.2">itsx</requirement>
</expand>
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6 changes: 6 additions & 0 deletions tools/frogs/macros.xml
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<macros>
<token name="@TOOL_VERSION@">4.1.0</token>
<token name="@VERSION_SUFFIX@">3</token>

<xml name="xrefs">
<xrefs>
<xref type="bio.tools">frogs</xref>
</xrefs>
</xml>

<xml name="requirements">
<requirements>
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1 change: 1 addition & 0 deletions tools/frogs/normalisation.xml
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<macros>
<import>macros.xml</import>
</macros>
<expand macro="xrefs"/>
<expand macro="requirements"/>

<stdio>
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1 change: 1 addition & 0 deletions tools/frogs/phyloseq_alpha_diversity.xml
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<macros>
<import>macros.xml</import>
</macros>
<expand macro="xrefs"/>
<expand macro="requirements_phyloseq" />
<command detect_errors="exit_code">
phyloseq_alpha_diversity.py
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1 change: 1 addition & 0 deletions tools/frogs/phyloseq_beta_diversity.xml
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<macros>
<import>macros.xml</import>
</macros>
<expand macro="xrefs"/>
<expand macro="requirements_phyloseq">
<requirement type="package" version="2.3">r-gridextra</requirement>
</expand>
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1 change: 1 addition & 0 deletions tools/frogs/phyloseq_clustering.xml
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<macros>
<import>macros.xml</import>
</macros>
<expand macro="xrefs"/>
<expand macro="requirements_phyloseq" />
<command detect_errors="exit_code">
phyloseq_clustering.py
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1 change: 1 addition & 0 deletions tools/frogs/phyloseq_composition.xml
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<macros>
<import>macros.xml</import>
</macros>
<expand macro="xrefs"/>
<expand macro="requirements_phyloseq">
<requirement type="package" version="4.9.3">r-plotly</requirement>
</expand>
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1 change: 1 addition & 0 deletions tools/frogs/phyloseq_import_data.xml
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<macros>
<import>macros.xml</import>
</macros>
<expand macro="xrefs"/>
<expand macro="requirements_phyloseq" />
<command detect_errors="exit_code">
phyloseq_import_data.py
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1 change: 1 addition & 0 deletions tools/frogs/phyloseq_manova.xml
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<macros>
<import>macros.xml</import>
</macros>
<expand macro="xrefs"/>
<expand macro="requirements_phyloseq" />
<command detect_errors="exit_code">
phyloseq_manova.py
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1 change: 1 addition & 0 deletions tools/frogs/phyloseq_structure.xml
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<macros>
<import>macros.xml</import>
</macros>
<expand macro="xrefs"/>
<expand macro="requirements_phyloseq" >
<requirement type="package" version="4.9.3">r-plotly</requirement>
</expand>
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1 change: 1 addition & 0 deletions tools/frogs/preprocess.xml
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<macros>
<import>macros.xml</import>
</macros>
<expand macro="xrefs"/>
<expand macro="requirements">
<requirement type="package" version="2.17.0">vsearch</requirement>
<requirement type="package" version="1.2.11">flash</requirement>
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1 change: 1 addition & 0 deletions tools/frogs/remove_chimera.xml
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<macros>
<import>macros.xml</import>
</macros>
<expand macro="xrefs"/>
<expand macro="requirements">
<requirement type="package" version="2.17.0">vsearch</requirement>
</expand>
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1 change: 1 addition & 0 deletions tools/frogs/taxonomic_affiliation.xml
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<macros>
<import>macros.xml</import>
</macros>
<expand macro="xrefs"/>
<expand macro="requirements">
<requirement type="package" version="2.10">blast</requirement>
<requirement type="package" version="6.6.0">emboss</requirement>
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1 change: 1 addition & 0 deletions tools/frogs/tree.xml
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<macros>
<import>macros.xml</import>
</macros>
<expand macro="xrefs"/>
<expand macro="requirements">
<requirement type="package" version="7.407">mafft</requirement>
<requirement type="package" version="2.1.9">fasttree</requirement>
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1 change: 1 addition & 0 deletions tools/frogs/tsv_to_biom.xml
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<macros>
<import>macros.xml</import>
</macros>
<expand macro="xrefs"/>
<expand macro="requirements" />
<command detect_errors="exit_code">
tsv_to_biom.py
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