| Previous changeset 9:abf9ed143b04 (2025-05-05) |
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Commit message:
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit a84c70b1ba1bc65672b93387964d04bcd9435c44 |
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modified:
frogsfunc_pathways.xml frogsfunc_placeseqs.xml macros.xml normalisation.xml phyloseq_alpha_diversity.xml phyloseq_beta_diversity.xml phyloseq_clustering.xml phyloseq_composition.xml phyloseq_import_data.xml phyloseq_manova.xml phyloseq_structure.xml preprocess.xml remove_chimera.xml |
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removed:
normalisation.xml.bak |
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| diff -r abf9ed143b04 -r ea59fac8fa17 frogsfunc_pathways.xml --- a/frogsfunc_pathways.xml Mon May 05 12:58:24 2025 +0000 +++ b/frogsfunc_pathways.xml Wed May 07 09:45:13 2025 +0000 |
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| @@ -25,7 +25,7 @@ <expand macro="requirements_frogsfunc" /> <command detect_errors="exit_code"> - [<![CDATA[ + <![CDATA[ frogsfunc_pathways.py --input-file $input_file |
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| diff -r abf9ed143b04 -r ea59fac8fa17 frogsfunc_placeseqs.xml --- a/frogsfunc_placeseqs.xml Mon May 05 12:58:24 2025 +0000 +++ b/frogsfunc_placeseqs.xml Wed May 07 09:45:13 2025 +0000 |
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| @@ -27,7 +27,7 @@ </expand> <command detect_errors="exit_code"> - [<![CDATA[ + <![CDATA[ frogsfunc_placeseqs.py --input-fasta $input_fasta --input-biom $input_biom |
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| diff -r abf9ed143b04 -r ea59fac8fa17 macros.xml --- a/macros.xml Mon May 05 12:58:24 2025 +0000 +++ b/macros.xml Wed May 07 09:45:13 2025 +0000 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">4.2.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="requirements"> <requirements> |
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| diff -r abf9ed143b04 -r ea59fac8fa17 normalisation.xml --- a/normalisation.xml Mon May 05 12:58:24 2025 +0000 +++ b/normalisation.xml Wed May 07 09:45:13 2025 +0000 |
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| @@ -24,7 +24,7 @@ <expand macro="requirements"/> <command detect_errors="exit_code"> - [<![CDATA[ + <![CDATA[ normalisation.py --input-biom '$input_biom' --input-fasta '$input_fasta' |
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| diff -r abf9ed143b04 -r ea59fac8fa17 normalisation.xml.bak --- a/normalisation.xml.bak Mon May 05 12:58:24 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,148 +0,0 @@ -<?xml version="1.0"?> -<!-- -# Copyright (C) 2015 INRA -# -# This program is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program. If not, see <http://www.gnu.org/licenses/>. ---> -<tool id="FROGS_normalisation" name="FROGS Abundance normalisation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> - <description>Normalise ASV abundance. </description> - - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"/> - - <command detect_errors="exit_code"> - [<![CDATA[ - normalisation.py - --input-biom '$input_biom' - --input-fasta '$input_fasta' - - #if $sampling_method.sampling_by_min == "yes" - --sampling-by-min - #else - --num-reads '$sampling_method.num_reads' - - #if $sampling_method.delete_samples == "true" - --delete-samples - #end if - #end if - - --output-biom '$output_biom' - --output-fasta '$output_fasta' - --summary-file '$summary_file' - ]]> - </command> - <inputs> - <param format="fasta" argument="--input-fasta" type="data" label="Sequence file" help="Sequence file to normalise (format: fasta)." /> - <param format="biom1" argument="--input-biom" type="data" label="Abundance file" help="Abundance file to normalise (format: BIOM)." /> - <conditional name="sampling_method"> - <param argument="--sampling-by-min" type="select" label="Sampling method" help="Sampling by the number of sequences of the smallest sample, or select a number manually" display="radio"> - <option value="yes" selected="true">Sampling by the number of sequences of the smallest sample</option> - <option value="no">Select a number of sequences</option> - </param> - <when value="yes"/> - <when value="no"> - <param argument="--num-reads" type="integer" optional="true" min="1" value="" label="Number of reads" help="The final number of reads per sample." /> - <param argument="--delete-samples" type="select" label="Remove samples that have an initial number of reads below the number of reads to sample ?" display="radio"> - <option value="false">No, subsampling threshold need to at most equal to the smallest sample</option> - <option value="true">Yes, subsampling threshold may be greater than the smallest sample</option> - </param> - </when> - </conditional> - </inputs> - <outputs> - <data format="fasta" name="output_fasta" label="${tool.name}: normalised_sequences.fasta" from_work_dir="normalised.fasta" /> - <data format="biom1" name="output_biom" label="${tool.name}: normalised_abundance.biom" from_work_dir="normalised.biom" /> - <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html" /> - </outputs> - <tests> - <test> - <param name="input_fasta" value="references/08-affiliation_postprocessed.fasta"/> - <param name="input_biom" value="references/08-affiliation_postprocessed.biom"/> - <conditional name="sampling_method"> - <param name="sampling_by_min" value="no"/> - <param name="num_reads" value="100"/> - </conditional> - <output name="summary_file" file="references/09-normalisation.html" compare="sim_size" delta="0" /> - <output name="summary_file" file="references/09-normalisation.html" compare="diff" lines_diff="4" /> - <output name="output_fasta" file="references/09-normalisation.fasta" compare="diff" lines_diff="12" /> - </test> - </tests> - <help> - -@HELP_LOGO@ - -.. class:: infomark page-header h2 - -What it does - -This tool keeps, in each sample, the same number of elements by random sampling. - -.. class:: infomark page-header h2 - -Inputs/outputs - -.. class:: h3 - -Inputs - -**Sequence file**: - -The sequences (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). - -**Abundance file**: - -The abundance of each ASV in each sample (format `BIOM <http://biom-format.org/>`_). - -**Sampling method**: - -Sequence normalisation method : - - - **Sampling by the number of sequences of the smallest sample** : Automatically detects the number of sequences of the smallest sample, and selects this number for all other samples. - - **Select number of sequences** : Manually select a number of sequences. - -With this number, a random draw of sequences is made and once normalisation is complete, each sample will contain the specified number of sequences. - -.. class:: warningmark - -If the **remove samples** option is enabled, samples whose total number of sequences is lower than the specified number will be removed inside the abundance table. - -If the option is disabled, the samples will be kept in the analysis but with a number of sequences lower than the specified number (the total number of the sample). - -.. class:: h3 - -Outputs - -**Sequence file** (normalised_seed.fasta): - - The normalised sequence file (format `FASTA <https://en.wikipedia.org/wiki/FASTA_format>`_). - -**Abundance file** (normalised_abundance.biom): - - The normalised abundance file. If option **remove samples** has been chosen, then the abundance table will no longer contain information about the removed samples. (format `BIOM <http://biom-format.org/>`_). - -**Report file** (report.html): - - Information about discarded data (format `HTML <https://en.wikipedia.org/wiki/HTML>`_). - - -.. class:: infomark page-header h2 - - -@HELP_CONTACT@ - - </help> - <expand macro="citations" /> -</tool> |
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| diff -r abf9ed143b04 -r ea59fac8fa17 phyloseq_alpha_diversity.xml --- a/phyloseq_alpha_diversity.xml Mon May 05 12:58:24 2025 +0000 +++ b/phyloseq_alpha_diversity.xml Wed May 07 09:45:13 2025 +0000 |
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| @@ -5,7 +5,7 @@ </macros> <expand macro="requirements_phyloseq" /> <command detect_errors="exit_code"> - [<![CDATA[ + <![CDATA[ phyloseq_alpha_diversity.py --rdata '$data' --varExp '$varExp' |
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| diff -r abf9ed143b04 -r ea59fac8fa17 phyloseq_beta_diversity.xml --- a/phyloseq_beta_diversity.xml Mon May 05 12:58:24 2025 +0000 +++ b/phyloseq_beta_diversity.xml Wed May 07 09:45:13 2025 +0000 |
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| @@ -7,7 +7,7 @@ <requirement type="package" version="2.3">r-gridextra</requirement> </expand> <command detect_errors="exit_code"> - [<![CDATA[ + <![CDATA[ phyloseq_beta_diversity.py --rdata '$data' --varExp '$varExp' @@ -58,7 +58,7 @@ <param name="varExp" value="EnvType"/> <param name="methods" value="cc,unifrac"/> <!-- sinon test le nombre de fois où il y a img src= on en attend 2 --> - <output name="html" file="references/19-phylo_beta_div.nb.html" compare="diff" lines_diff="0" count="2" /> + <output name="html" file="references/19-phylo_beta_div.nb.html" compare="diff" lines_diff="0" count="3" /> <output name="html"> <discovered_dataset designation="unifrac.tsv" ftype="tsv" file="references/unifrac.tsv" compare="diff" lines_diff="0"/> </output> |
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| diff -r abf9ed143b04 -r ea59fac8fa17 phyloseq_clustering.xml --- a/phyloseq_clustering.xml Mon May 05 12:58:24 2025 +0000 +++ b/phyloseq_clustering.xml Wed May 07 09:45:13 2025 +0000 |
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| @@ -5,7 +5,7 @@ </macros> <expand macro="requirements_phyloseq" /> <command detect_errors="exit_code"> - [<![CDATA[ + <![CDATA[ phyloseq_clustering.py --html '$html' --rdata '$data' |
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| diff -r abf9ed143b04 -r ea59fac8fa17 phyloseq_composition.xml --- a/phyloseq_composition.xml Mon May 05 12:58:24 2025 +0000 +++ b/phyloseq_composition.xml Wed May 07 09:45:13 2025 +0000 |
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| @@ -7,7 +7,7 @@ <requirement type="package" version="4.9.3">r-plotly</requirement> </expand> <command detect_errors="exit_code"> - [<![CDATA[ + <![CDATA[ phyloseq_composition.py --rdata '$data' --varExp '$varExp' |
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| diff -r abf9ed143b04 -r ea59fac8fa17 phyloseq_import_data.xml --- a/phyloseq_import_data.xml Mon May 05 12:58:24 2025 +0000 +++ b/phyloseq_import_data.xml Wed May 07 09:45:13 2025 +0000 |
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| @@ -5,7 +5,7 @@ </macros> <expand macro="requirements_phyloseq" /> <command detect_errors="exit_code"> - [<![CDATA[ + <![CDATA[ phyloseq_import_data.py --biomfile '$biomfile' --samplefile '$samplefile' |
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| diff -r abf9ed143b04 -r ea59fac8fa17 phyloseq_manova.xml --- a/phyloseq_manova.xml Mon May 05 12:58:24 2025 +0000 +++ b/phyloseq_manova.xml Wed May 07 09:45:13 2025 +0000 |
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| @@ -5,7 +5,7 @@ </macros> <expand macro="requirements_phyloseq" /> <command detect_errors="exit_code"> - [<![CDATA[ + <![CDATA[ phyloseq_manova.py --rdata '$data' --varExp '$varExp' |
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| diff -r abf9ed143b04 -r ea59fac8fa17 phyloseq_structure.xml --- a/phyloseq_structure.xml Mon May 05 12:58:24 2025 +0000 +++ b/phyloseq_structure.xml Wed May 07 09:45:13 2025 +0000 |
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| @@ -7,7 +7,7 @@ <requirement type="package" version="4.9.3">r-plotly</requirement> </expand> <command detect_errors="exit_code"> - [<![CDATA[ + <![CDATA[ phyloseq_structure.py --html '$html' --rdata '$data' |
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| diff -r abf9ed143b04 -r ea59fac8fa17 preprocess.xml --- a/preprocess.xml Mon May 05 12:58:24 2025 +0000 +++ b/preprocess.xml Wed May 07 09:45:13 2025 +0000 |
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| @@ -9,7 +9,7 @@ <requirement type="package" version="2.10">cutadapt</requirement> </expand> <command detect_errors="exit_code"> - [<![CDATA[ + <![CDATA[ preprocess.py '$sequencer_type.sequencer_selected' --output-dereplicated '$dereplicated_file' --output-count '$count_file' --summary '$summary_file' @CPUS@ |
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| diff -r abf9ed143b04 -r ea59fac8fa17 remove_chimera.xml --- a/remove_chimera.xml Mon May 05 12:58:24 2025 +0000 +++ b/remove_chimera.xml Wed May 07 09:45:13 2025 +0000 |
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| @@ -7,7 +7,7 @@ <requirement type="package" version="2.17.0">vsearch</requirement> </expand> <command detect_errors="exit_code"> - [<![CDATA[ + <![CDATA[ remove_chimera.py @CPUS@ --input-fasta '$sequence_file' --non-chimera '$non_chimera_fasta' |