Mercurial > repos > bcclaywell > microbiome_pplacer_suite
changeset 6:3c50a937d7c1 draft
Uploaded
author | bcclaywell |
---|---|
date | Wed, 15 Apr 2015 19:14:23 -0400 |
parents | 2d023c621bd0 |
children | b6ece07bec6a |
files | alignment.xml bootstrap.xml classification.xml decorate.xml filter.xml macros.xml pplacer.xml preclassification.xml preprocessing.xml refpkgzip_to_refpkg.xml render_datatable.xml usearch.xml |
diffstat | 12 files changed, 133 insertions(+), 73 deletions(-) [+] |
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--- a/alignment.xml Thu Mar 26 16:56:09 2015 -0400 +++ b/alignment.xml Wed Apr 15 19:14:23 2015 -0400 @@ -1,18 +1,18 @@ <tool id="PHYLO_alignment" name="Align query sequences" version="1.0.0"> <description>with sequences in a reference package</description> - <requirements> - <requirement type="package">yapp_env</requirement> - </requirements> <macros> <import>macros.xml</import> </macros> - <version_command>echo "guppy $(guppy --version)"</version_command> + <requirements> + <requirement type="package">yapp_env</requirement> + </requirements> + <stdio> + <expand macro="basic_errors"/> + </stdio> + <version_command>echo "$(taxit -V); $(cmalign -h | grep INFERNAL); $(esl-alimerge -h | grep Easel)"</version_command> <command interpreter="bash"> alignment-wrapper.sh ${config} </command> - <stdio> - <expand macro="basic_errors"/> - </stdio> <inputs> <param name="refpkg" type="data" format="refpkg" label="Reference package"/> <param name="input_seqs" type="data" format="fasta" label="Input sequences"/> @@ -44,4 +44,8 @@ reference sequences. </help> + <citations> + <expand macro="cite_taxtastic"/> + <expand macro="cite_infernal"/> + </citations> </tool>
--- a/bootstrap.xml Thu Mar 26 16:56:09 2015 -0400 +++ b/bootstrap.xml Wed Apr 15 19:14:23 2015 -0400 @@ -1,18 +1,18 @@ <tool id="PHYLO_bootstrap" name="Prepare data" version="1.1.0"> <description>for analysis</description> + <macros> + <import>macros.xml</import> + </macros> <requirements> <requirement type="package">yapp_env</requirement> </requirements> - <macros> - <import>macros.xml</import> - </macros> + <stdio> + <expand macro="basic_errors"/> + </stdio> <version_command>echo "bootstrap script 1.1.0"</version_command> <command interpreter="bash"> bootstrap-wrapper.sh $config </command> - <stdio> - <expand macro="basic_errors"/> - </stdio> <inputs> <param name="plate_id" type="integer" value="1" label="Plate number"/> <conditional name="run_type">
--- a/classification.xml Thu Mar 26 16:56:09 2015 -0400 +++ b/classification.xml Wed Apr 15 19:14:23 2015 -0400 @@ -1,18 +1,18 @@ <tool id="PHYLO_classification" name="Output classifications" version="2.1.0"> <description>in tabular format</description> - <requirements> - <requirement type="package">yapp_env</requirement> - </requirements> <macros> <import>macros.xml</import> </macros> - <version_command>echo "guppy $(guppy --version)"</version_command> + <requirements> + <requirement type="package">yapp_env</requirement> + </requirements> + <stdio> + <expand macro="basic_errors"/> + </stdio> + <version_command>echo "pplacer $(pplacer --version)"</version_command> <command interpreter="bash"> classification-wrapper.sh ${config} </command> - <stdio> - <expand macro="basic_errors"/> - </stdio> <inputs> <param name="split_map" type="data" format="csv" label="Read-to-specimen map"/> <param name="label_map" type="data" format="csv" label="Specimen-to-label map"/> @@ -101,4 +101,7 @@ GLKT0ZE01CQ2BU below_species species 341694 0.073214 </help> + <citations> + <expand macro="cite_pplacer"/> + </citations> </tool>
--- a/decorate.xml Thu Mar 26 16:56:09 2015 -0400 +++ b/decorate.xml Wed Apr 15 19:14:23 2015 -0400 @@ -1,18 +1,18 @@ <tool id="PHYLO_decorate" name="Decorate" version="1.0.0"> <description>classification results with sample metadata</description> + <macros> + <import>macros.xml</import> + </macros> <requirements> <requirement type="package">yapp_env</requirement> </requirements> - <macros> - <import>macros.xml</import> - </macros> + <stdio> + <expand macro="basic_errors"/> + </stdio> <version_command>echo "decorate script 1.0.0"</version_command> <command interpreter="bash"> decorate-wrapper.sh ${config} </command> - <stdio> - <expand macro="basic_errors"/> - </stdio> <inputs> <param name="group_by_specimen" type="data" format="csv" label="Grouped-by-specimen classification"/> <param name="metadata" type="data" format="csv" label="Sample metadata"/>
--- a/filter.xml Thu Mar 26 16:56:09 2015 -0400 +++ b/filter.xml Wed Apr 15 19:14:23 2015 -0400 @@ -1,18 +1,18 @@ <tool id="PHYLO_filter" name="Filter and trim" version="1.2.0"> <description>sequences</description> + <macros> + <import>macros.xml</import> + </macros> <requirements> <requirement type="package">yapp_env</requirement> </requirements> - <macros> - <import>macros.xml</import> - </macros> + <stdio> + <expand macro="basic_errors"/> + </stdio> <version_command>seqmagick --version</version_command> <command interpreter="bash"> filter-wrapper.sh ${config} </command> - <stdio> - <expand macro="basic_errors"/> - </stdio> <inputs> <!-- TODO: can take either fasta+qual or fastq --> <param name="plate_id" type="integer" value="1" label="Plate number"/> @@ -100,4 +100,8 @@ .. _quality filter documentation: http://fhcrc.github.io/seqmagick/quality_filter.html </help> + <citations> + <expand macro="cite_seqmagick"/> + <expand macro="cite_biopython"/> + </citations> </tool>
--- a/macros.xml Thu Mar 26 16:56:09 2015 -0400 +++ b/macros.xml Wed Apr 15 19:14:23 2015 -0400 @@ -5,4 +5,49 @@ <regex match="traceback" level="fatal"/> <regex match="warning" level="warning"/> </macro> + <macro name="cite_seqmagick"> + <citation type="bibtex">@MISC{fhcrc_seqmagick, + title = {seqmagick: An imagemagick-like frontend to Biopython SeqIO}, + author = {McCoy, C. O. and Hodges, B. and Rosenthal, C. and Gallagher, A. and Matsen, IV, F. A.}, + publisher = {GitHub}, + url = "http://github.com/fhcrc/seqmagick", + note = "version 0.5.0" +} + </citation> + </macro> + <!-- Biopython 1.63 --> + <macro name="cite_biopython"> + <citation type="doi">10.1093/bioinformatics/btp163</citation> + </macro> + <macro name="cite_taxtastic"> + <citation type="bibtex">@MISC{fhcrc_taxtastic, + title = {taxtastic: Create and maintain phylogenetic "reference packages" of biological sequences}, + author = {McCoy, C. O. and Hoffman, N. G. and Gallagher, A. and Hodges, B. and Ross, F. and Matsen, IV, F. A.}, + publisher = {GitHub}, + url = "http://github.com/fhcrc/taxtastic", + note = "version 0.5.2" +} + </citation> + </macro> + <!-- INFERNAL 1.1 --> + <macro name="cite_infernal"> + <citation type="doi">10.1093/bioinformatics/btt509</citation> + </macro> + <!-- pplacer 1.1alpha + (the citation is for pplacer 1.0) --> + <macro name="cite_pplacer"> + <citation type="doi">10.1186/1471-2105-11-538</citation> + <citation type="bibtex">@MISC{fhcrc_pplacer, + title = {pplacer: Phylogenetic placement and downstream analysis}, + author = {Gallagher, A. and McCoy, C. O. and Claywell, B. C. and Small, C. T. and Hodges, B. and Hoffman, N. G. and Matsen, IV, F. A.}, + publisher = {GitHub}, + url = "http://github.com/matsen/pplacer", + note = "version v1.1.alpha16-1-gf748c91" +} + </citation> + </macro> + <!-- USEARCH 6 --> + <macro name="cite_usearch"> + <citation type="doi">10.1093/bioinformatics/btq461</citation> + </macro> </macros>
--- a/pplacer.xml Thu Mar 26 16:56:09 2015 -0400 +++ b/pplacer.xml Wed Apr 15 19:14:23 2015 -0400 @@ -1,18 +1,18 @@ <tool id="PHYLO_pplacer" name="Place aligned sequences" version="1.0.0"> <description>on a reference tree</description> + <macros> + <import>macros.xml</import> + </macros> <requirements> <requirement type="package">yapp_env</requirement> </requirements> - <macros> - <import>macros.xml</import> - </macros> + <stdio> + <expand macro="basic_errors"/> + </stdio> <version_command>echo "pplacer $(pplacer --version)"</version_command> <command interpreter="bash"> pplacer-wrapper.sh ${config} </command> - <stdio> - <expand macro="basic_errors"/> - </stdio> <inputs> <param name="refpkg" type="data" format="refpkg" label="Reference package"/> <param name="query_seqs" type="data" format="fasta" label="Query alignment"/> @@ -41,13 +41,8 @@ according to a reference alignment, producing taxonomic annotations which can be used for classification and visualization. ------ - -**Citation** - -Matsen F, Kodner R, Armbrust E V: **pplacer: linear time maximum-likelihood and -Bayesian phylogenetic placement of sequences onto a fixed reference tree**. BMC -Bioinformatics 2010, **11**:1. - </help> + <citations> + <expand macro="cite_pplacer"/> + </citations> </tool>
--- a/preclassification.xml Thu Mar 26 16:56:09 2015 -0400 +++ b/preclassification.xml Wed Apr 15 19:14:23 2015 -0400 @@ -1,18 +1,18 @@ <tool id="PHYLO_preclassification" name="Generate database" version="1.2.0"> <description>for classification</description> - <requirements> - <requirement type="package">yapp_env</requirement> - </requirements> <macros> <import>macros.xml</import> </macros> - <version_command>echo "guppy $(guppy --version)"</version_command> + <requirements> + <requirement type="package">yapp_env</requirement> + </requirements> + <stdio> + <expand macro="basic_errors"/> + </stdio> + <version_command>echo "pplacer $(pplacer --version)"</version_command> <command interpreter="bash"> preclassification-wrapper.sh ${config} </command> - <stdio> - <expand macro="basic_errors"/> - </stdio> <inputs> <param name="dedup_info" type="data" format="csv" label="Deduplication info"/> <param name="refpkg" type="data" format="refpkg" label="Reference package"/> @@ -47,4 +47,7 @@ in taxonomic classification. </help> + <citations> + <expand macro="cite_pplacer"/> + </citations> </tool>
--- a/preprocessing.xml Thu Mar 26 16:56:09 2015 -0400 +++ b/preprocessing.xml Wed Apr 15 19:14:23 2015 -0400 @@ -1,18 +1,18 @@ <tool id="PHYLO_preprocessing" name="Deduplicate sequences" version="3.0.0"> <description>in preparation for alignment and placement</description> - <requirements> - <requirement type="package">yapp_env</requirement> - </requirements> <macros> <import>macros.xml</import> </macros> - <version_command>echo "guppy $(guppy --version)"</version_command> + <requirements> + <requirement type="package">yapp_env</requirement> + </requirements> + <stdio> + <expand macro="basic_errors"/> + </stdio> + <version_command>echo "pplacer $(pplacer --version)"</version_command> <command interpreter="bash"> preprocessing-wrapper.sh ${config} </command> - <stdio> - <expand macro="basic_errors"/> - </stdio> <inputs> <param name="input_seqs" type="data" format="fasta" label="Input sequences"/> <param name="split_map" type="data" format="csv" label="Read-to-specimen map"/> @@ -42,4 +42,7 @@ This tool deduplicates input sequences in preparation for alignment and placement. </help> + <citations> + <expand macro="cite_pplacer"/> + </citations> </tool>
--- a/refpkgzip_to_refpkg.xml Thu Mar 26 16:56:09 2015 -0400 +++ b/refpkgzip_to_refpkg.xml Wed Apr 15 19:14:23 2015 -0400 @@ -7,5 +7,12 @@ <data name="output" format="refpkg"/> </outputs> <help> + +.. class:: infomark + +**What it does** + +This tool unpacks a reference package from a ZIP file. + </help> </tool>
--- a/render_datatable.xml Thu Mar 26 16:56:09 2015 -0400 +++ b/render_datatable.xml Wed Apr 15 19:14:23 2015 -0400 @@ -3,12 +3,12 @@ <macros> <import>macros.xml</import> </macros> + <stdio> + <expand macro="basic_errors"/> + </stdio> <command interpreter="bash"> render_datatable-wrapper.sh $config </command> - <stdio> - <expand macro="basic_errors"/> - </stdio> <inputs> <param name="input" type="data" format="csv" label="CSV file"/> </inputs>
--- a/usearch.xml Thu Mar 26 16:56:09 2015 -0400 +++ b/usearch.xml Wed Apr 15 19:14:23 2015 -0400 @@ -3,13 +3,13 @@ <macros> <import>macros.xml</import> </macros> + <stdio> + <expand macro="basic_errors"/> + </stdio> <version_command>/home/matsengrp/local/bin/usearch6_64 --version</version_command> <command interpreter="bash"> usearch-wrapper.sh $config </command> - <stdio> - <expand macro="basic_errors"/> - </stdio> <inputs> <param name="input_seqs" type="data" format="fasta" label="Input sequences"/> <param name="class_db" type="data" format="sqlite3" label="Placement database"/> @@ -39,12 +39,8 @@ This tool queries large sequence databases for target sequences and assigns those sequences to clusters. ------ - -**Citation** - -Edgar, R C: **Search and clustering orders of magnitude faster than -BLAST**. Bioinformatics 2010, **26**:19. - </help> + <citations> + <expand macro="cite_usearch"/> + </citations> </tool>