comparison macros.xml @ 6:dbbe1ea8ecb1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"

5:8599fd07d140

    <xml name="version_command">
        <version_command><![CDATA[python -c "import scanpy as sc;print('scanpy version: %s' % sc.__version__)"]]></version_command>
    </xml>
    <token name="@CMD@"><![CDATA[
cp '$adata' 'anndata.h5ad' &&
cat '$script_file' &&
python '$script_file' &&
ls .
    ]]>
    </token>
    <token name="@CMD_imports@"><![CDATA[
import scanpy as sc
import pandas as pd
import numpy as np
    ]]>
    </token>

    </xml>
    <token name="@CMD_read_inputs@"><![CDATA[
adata = sc.read('anndata.h5ad')
]]>
    </token>
    <xml name="anndata_outputs">
        <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/>
    </xml>
    <token name="@CMD_anndata_write_outputs@"><![CDATA[
adata.write('anndata.h5ad')
]]>
    </token>
    <xml name="svd_solver">
        <param name="svd_solver" type="select" label="SVD solver to use" help="">
            <option value="auto">Automatically chosen depending on the size of the problem</option>
            <option value="arpack">ARPACK wrapper in SciPy</option>
            <option value="randomized">Randomized algorithm due to Halko (2009)</option>

6:dbbe1ea8ecb1

    <xml name="version_command">
        <version_command><![CDATA[python -c "import scanpy as sc;print('scanpy version: %s' % sc.__version__)"]]></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 sys
sys.stderr = open('$hidden_output', 'a')

import scanpy as sc
import pandas as pd
import numpy as np
    ]]>
    </token>

    </xml>
    <token name="@CMD_read_inputs@"><![CDATA[
adata = sc.read('anndata.h5ad')
]]>
    </token>
    <xml name="inputs_common_advanced">
        <section name="advanced_common" title="Advanced 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="${tool.name} (${method.method}) 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('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>
    <xml name="svd_solver">
        <param name="svd_solver" type="select" label="SVD solver to use" help="">
            <option value="auto">Automatically chosen depending on the size of the problem</option>
            <option value="arpack">ARPACK wrapper in SciPy</option>
            <option value="randomized">Randomized algorithm due to Halko (2009)</option>