annotate seurat_convert.xml @ 0:970696a7ae0b draft

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

<tool id="seurat_convert" name="Seurat 3 converter" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
    <description>translates different single cell formats</description>
    <macros>
        <import>seurat_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version" />
    <command detect_errors="exit_code"><![CDATA[
seurat-convert.R
@INPUT_OBJECT@
@OUTPUT_OBJECT@
]]></command>
    <inputs>
      <expand macro="input_object_params"/>
      <expand macro="output_object_params"/>
    </inputs>

    <outputs>
      <expand macro="output_files"/>
    </outputs>

    <tests>
        <test>
          <conditional name="input">
            <param name="format" value="rds_seurat"/>
            <param name="rds_seurat_file" value="E-MTAB-6077-3k_features_90_cells.rds"/>
          </conditional>
          <param name="format" value="loom"/>
          <output name="loom_file">
            <assert_contents>
              <has_h5_keys keys="layers,matrix,row_attrs"/>
            </assert_contents>
          </output>
        </test>
        <test>
          <conditional name="input">
            <param name="format" value="rds_seurat"/>
            <param name="rds_seurat_file" value="E-MTAB-6077-3k_features_90_cells.rds"/>
          </conditional>
          <param name="format" value="rds_sce"/>
          <output name="rds_sce_file">
            <assert_contents>
              <has_size value="2368166" delta="200000"/>
            </assert_contents>
          </output>
        </test>
        <test>
          <conditional name="input">
            <param name="format" value="loom"/>
            <param name="loom_file" value="E-MTAB-6077-3k_features_90_cells_loom.h5" ftype="h5"/>
          </conditional>
          <param name="format" value="rds_sce"/>
          <output name="rds_sce_file">
            <assert_contents>
              <has_size value="2432700" delta="200000"/>
            </assert_contents>
          </output>
        </test>
        <test>
          <conditional name="input">
            <param name="format" value="rds_sce"/>
            <param name="rds_sce_file" value="E-MTAB-6077-3k_features_90_cells_sce.rds" ftype="rdata.sce"/>
          </conditional>
          <param name="format" value="rds_seurat"/>
          <output name="rds_seurat_file">
            <assert_contents>
              <has_size value="2366603" delta="200000"/>
            </assert_contents>
          </output>
        </test>
        <test>
          <conditional name="input">
            <param name="format" value="anndata"/>
            <param name="anndata_file" value="E-MTAB-6077-3k_features_90_cells.h5ad" ftype="h5ad"/>
          </conditional>
          <param name="format" value="rds_seurat"/>
          <output name="rds_seurat_file">
            <assert_contents>
              <has_size value="2965562" delta="200000"/>
            </assert_contents>
          </output>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**

This tool uses Seurat 3 to convert formats. Possible inputs are:

    * Seurat 3
    * Loom (probably earlier than Loom 3.0)
    * AnnData (contemporary versions to Seurat 3, most likely up to AnnData 0.6.22.post1)
    * Single Cell Experiment

Possible outputs are:

    * Seurat 3
    * Loom (as produced by loomR package)
    * Single Cell Experiment

For newer versions of AnnData and Loom, please try the Seurat 4 version of this tool.

@SEURAT_INTRO@


.. _Seurat: https://www.nature.com/articles/nbt.4096
.. _Satija Lab: https://satijalab.org/seurat/

@VERSION_HISTORY@

]]></help>
      <expand macro="citations" />
</tool>