annotate macros.xml @ 1:fe5996e87b41 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit d1eee788f207ac0077cb5fea82a3f32cc4980e40

<macros>
    <token name="@TOOL_VERSION@">1.0.1</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@profile@">22.05</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">cosg</requirement>
            <requirement type="package" version="1.9.8">scanpy</requirement>
            <requirement type="package" version="1.5.3">pandas</requirement>
            <requirement type="package" version="3.7">matplotlib</requirement>
            <requirement type="package" version="0.12.2">seaborn</requirement>
            <yield />
        </requirements>
    </xml>
    <xml name="creators">
        <creator>
            <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" />
        </creator>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/bib/bbab579</citation>
            <citation type="doi">10.1093/gigascience/giaa102</citation>
        </citations>
    </xml>
    <xml name="version_command">
        <version_command><![CDATA[python -c "import cosg;import importlib.metadata;print('%s' % importlib.metadata.version('cosg'))"]]></version_command>
    </xml>
    <token name="@CMD@"><![CDATA[
cp '$adata' 'anndata.h5ad' &&
cat '$script_file' > '$hidden_output' &&
python '$script_file' >> '$hidden_output' &&
ls . >> '$hidden_output' &&
touch 'anndata_info.txt' &&
cat 'anndata_info.txt' @CMD_prettify_stdout@
    ]]>
    </token>
    <token name="@CMD_imports@"><![CDATA[
import scanpy as sc
import pandas as pd
import numpy as np
import cosg
    ]]>
    </token>
    <xml name="sanitize_query" token_validinitial="string.printable">
        <sanitizer>
            <valid initial="@VALIDINITIAL@">
                <remove value="&apos;" />
            </valid>
       </sanitizer>
    </xml>
    <xml name="sanitize_vectors" token_validinitial="string.digits">
        <sanitizer>
            <valid initial="@VALIDINITIAL@">
                <add value=","/>
            </valid>
        </sanitizer>
    </xml>
    <xml name="inputs_anndata">
        <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
    </xml>
    <token name="@CMD_read_inputs@"><![CDATA[
adata = sc.read_h5ad('anndata.h5ad')
]]>
    </token>
    <xml name="inputs_common_advanced">
        <section name="advanced_common" title="Advanced Output Options" expanded="false">
            <param name="show_log" type="boolean" checked="false" label="Output Log?" />
        </section>
    </xml>
    <xml name="anndata_outputs">
        <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} on ${on_string}: Annotated data matrix"/>
        <data name="hidden_output" format="txt" label="Log file" >
            <filter>advanced_common['show_log']</filter>
        </data>
    </xml>
    <token name="@CMD_anndata_write_outputs@"><![CDATA[
adata.write_h5ad('anndata.h5ad')
with open('anndata_info.txt','w', encoding='utf-8') as ainfo:
    print(adata, file=ainfo)
]]>
    </token>
    <token name="@CMD_prettify_stdout@"><![CDATA[ | sed -r '1 s|AnnData object with (.+) = (.*)\s*|\1: \2|g' | sed "s|'||g"  | sed -r 's|^\s*(.*):\s(.*)|[\1]\n-    \2|g' | sed 's|, |\n-    |g'
    ]]></token>
</macros>