annotate seurat_macros.xml @ 5:301cf1b4b43d draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 355bb52d2e9d170b1db237e649657cc14e0a047a"

<?xml version="1.0"?>
<macros>
    <token name="@VERSION@">0.3.0</token>
    <token name="@SEURAT_VERSION@">3.2.3</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">seurat-scripts</requirement>
        </requirements>
    </xml>
    <xml name="version">
    	<version_command><![CDATA[
echo $(R --version | grep version | grep -v GNU)", seurat version" $(R --vanilla --slave -e "library(seurat); cat(sessionInfo()\$otherPkgs\$seurat\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
    ]]></version_command>
    </xml>

   <xml name="input_object_params">
     <conditional name="input" label="Input format">
       <param type="select" name="format" label="Choose the format of the input" help="RData, Loom or AnnData">
         <option value="rds_seurat" selected="true">RDS with a Seurat object</option>
         <option value="loom">Loom</option>
         <option value="anndata">AnnData</option>
         <option value="rds_sce">RDS with a Single Cell Experiment object</option>
       </param>
       <when value="anndata">
         <param type="data" name="anndata_file" label="AnnData file" help="The AnnData format provided by Scanpy" format="h5,h5ad"/>
       </when>
       <when value="loom">
         <param type="data" name="loom_file" label="Loom file" help="Input as Loom v? file" format="h5,h5loom"/>
       </when>
       <when value="rds_seurat">
         <param type="data" name="rds_seurat_file" label="RDS file" help="Input as RDS file with Seurat 3 object" format="rdata"/>
       </when>
       <when value="rds_sce">
         <param type="data" name="rds_sce_file" label="RDS file" help="Input as RDS file with Single Cell Experiment object" format="rdata"/>
       </when>
     </conditional>
   </xml>

   <token name="@INPUT_OBJECT@">
    #if $input.format == "anndata"
        --input-object-file '$input.anndata_file' --input-format anndata
    #else if $input.format == "loom"
        --input-object-file '$input.loom_file' --input-format loom
    #else if $input.format == "rds_seurat"
        --input-object-file '$input.rds_seurat_file' --input-format seurat
    #else if $input.format == "rds_sce"
        --input-object-file '$input.rds_sce_file' --input-format singlecellexperiment
    #end if
   </token>

   <xml name="output_object_params">
     <param type="select" name="format" label="Choose the format of the output" help="Seurat, Single Cell Experiment or Loom">
       <option value="rds_seurat" selected="true">RDS with a Seurat object</option>
       <option value="loom">Loom</option>
       <option value="rds_sce">RDS with a Single Cell Experiment object</option>
     </param>
   </xml>

   <xml name="output_files">
    <data name="loom_file" from_work_dir="seurat_obj.loom" format="h5" label="${tool.name} on ${on_string}: Seurat Loom">
      <filter>format == 'loom'</filter>
    </data>
    <data name="rds_seurat_file" format="rdata" label="${tool.name} on ${on_string}: Seurat RDS">
      <filter>format == 'rds_seurat'</filter>
    </data>
    <data name="rds_sce_file" format="rdata" label="${tool.name} on ${on_string}: Seurat Single Cell Experiment RDS">
      <filter>format == 'rds_sce'</filter>
    </data>
   </xml>

   <token name="@OUTPUT_OBJECT@">
    #if $format == "anndata"
        --output-object-file '$anndata_file' --output-format anndata
    #else if $format == "loom"
        --output-object-file seurat_obj.loom --output-format loom
    #else if $format == "rds_seurat"
        --output-object-file '$rds_seurat_file' --output-format seurat
    #else if $format == "rds_sce"
        --output-object-file '$rds_sce_file' --output-format singlecellexperiment
    #end if
   </token>

    <xml name="genes-use-input">
      <param name="genes_use" argument="--genes-use" optional="true" type="data" format="tsv,txt,tabular" label="Genes to use" help="A file with gene names to use in construction of SNN graph if building directly based on expression data rather than a dimensionally reduced representation (i.e. PCs)."/>
    </xml>
    <xml name="dims-use-input">
      <param name="dims_use" argument="--dims-use" min="1" optional="true" type="integer" label="PCA Dimensions to use" help="Number of PCs (dimensions) to use in construction of the SNN graph."/>
    </xml>

    <token name="@SEURAT_INTRO@"><![CDATA[
Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data.
It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and
interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse
types of single cell data.
      ]]></token>

    <token name="@VERSION_HISTORY@"><![CDATA[
**Version history**

3.2.3+galaxy0: Moves to Seurat 3.2.3 and introduce convert method, improving format interconversion support.

3.1.2_0.0.8: Update metadata parsing

3.1.1_0.0.7: Exposes perplexity and enables tab input.

3.1.1_0.0.6+galaxy0: Moved to Seurat 3.

  Find clusters: removed dims-use, k-param, prune-snn.

2.3.1+galaxy0: Improved documentation and further exposition of all script's options. Pablo Moreno, Jonathan Manning and Ni Huang, Expression Atlas team https://www.ebi.ac.uk/gxa/home  at
EMBL-EBI https://www.ebi.ac.uk/. Parts obtained from wrappers from Christophe Antoniewski(github.com/drosofff) and Lea Bellenger(github.com/bellenger-l).

0.0.1: Initial contribution. Maria Doyle (github.com/mblue9).
      ]]></token>


    <xml name="citations">
        <citations>
            <citation type="doi">10.1038/nbt.4096</citation>
            <citation type="bibtex">
              @misc{r-seurat-scripts.git,
              author = {Jonathan Manning, Pablo Moreno, EBI Gene Expression Team},
              year = {2018},
              title = {Seurat-scripts: command line interface for Seurat},
              publisher = {GitHub},
              journal = {GitHub repository},
              url = {https://github.com/ebi-gene-expression-group/r-seurat-scripts.git},
            }
            </citation>
            <citation type="doi">10.1038/s41592-021-01102-w</citation>
        </citations>
    </xml>
</macros>