comparison macros.xml @ 8:35bc2eb568ed draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 7b8af82cb8a3438d2a6535986e357527e5c6efec"

7:b2df381a6004

<macros>
    <token name="@version@">1.4.4.post1</token>
    <token name="@profile@">19.01</token>
    <token name="@galaxy_version@"><![CDATA[@version@+galaxy3]]></token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@version@">scanpy</requirement>
            <requirement type="package" version="2.0.17">loompy</requirement>
            <requirement type="package" version="2.9.0">h5py</requirement>
            <requirement type="package" version="0.7.0">leidenalg</requirement>
            <yield />
        </requirements>
    </xml>
    <xml name="citations">
        <citations>

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>

            </param>
            <param argument="linewidth" type="float" value="0" label="Width of the gray lines that frame the plot elements" help=""/>
            <param argument="color" type="select" label="Color for all of the elements" help="">
                <expand macro="matplotlib_color"/>
            </param>
            <param argument="palette" type="select" label="Colors to use for the different levels of the hue variable" help="">
                <expand macro="matplotlib_pyplot_colormap"/>
            </param>
            <param argument="saturation" type="float" value="0.75" min="0" max="1" label="Proportion of the original saturation to draw colors at" help=""/>
        </section>
    </xml>
    <token name="@CMD_params_seaborn_violinplot@"><![CDATA[
    bw='$method.seaborn_violinplot.bw',
#if $method.seaborn_violinplot.orient
    orient='$method.seaborn_violinplot.orient',
#end if
    linewidth=$method.seaborn_violinplot.linewidth,
    color='$method.seaborn_violinplot.color',
    palette='$method.seaborn_violinplot.palette',
    saturation=$method.seaborn_violinplot.saturation
    ]]></token>
    <xml name="param_color">
        <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes" help="One or a list of comma-separated index or key from either '.obs' or '.var'">
            <expand macro="sanitize_query" />

        <option value="drl">drl: Distributed Recursive Layout, pretty fast</option>
        <option value="rt">rt: Reingold Tilford tree layout</option>
        <option value="eq_tree">eq_tree: Equally spaced tree</option>
    </xml>
    <xml name="param_layout">
        <param argument="layout" type="select" label="Plotting layout" help="">
            <expand macro="options_layout"/>
        </param>
    </xml>
    <xml name="param_root">
        <param argument="root" type="text" value="" label="Comma-separated roots" help="If choosing a tree layout, this is the index of the root node or a list of root node indices. If this is a non-empty vector then the supplied node IDs are used as the roots of the trees (or a single tree if the graph is connected). If this is 'None' or an empty list, the root vertices are automatically calculated based on topological sorting.">

8:35bc2eb568ed

<macros>
    <token name="@version@">1.7.1</token>
    <token name="@profile@">19.01</token>
    <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@version@">scanpy</requirement>
            <requirement type="package" version="2.0.17">loompy</requirement>
            <requirement type="package" version="0.8.3">leidenalg</requirement>
            <yield />
        </requirements>
    </xml>
    <xml name="citations">
        <citations>

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
    ]]>
    </token>

            </param>
            <param argument="linewidth" type="float" value="0" label="Width of the gray lines that frame the plot elements" help=""/>
            <param argument="color" type="select" label="Color for all of the elements" help="">
                <expand macro="matplotlib_color"/>
            </param>
            <param argument="saturation" type="float" value="0.75" min="0" max="1" label="Proportion of the original saturation to draw colors at" help=""/>
        </section>
    </xml>
    <token name="@CMD_params_seaborn_violinplot@"><![CDATA[
    bw='$method.seaborn_violinplot.bw',
#if $method.seaborn_violinplot.orient
    orient='$method.seaborn_violinplot.orient',
#end if
    linewidth=$method.seaborn_violinplot.linewidth,
    color='$method.seaborn_violinplot.color',
    saturation=$method.seaborn_violinplot.saturation
    ]]></token>
    <xml name="param_color">
        <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes" help="One or a list of comma-separated index or key from either '.obs' or '.var'">
            <expand macro="sanitize_query" />

        <option value="drl">drl: Distributed Recursive Layout, pretty fast</option>
        <option value="rt">rt: Reingold Tilford tree layout</option>
        <option value="eq_tree">eq_tree: Equally spaced tree</option>
    </xml>
    <xml name="param_layout">
        <param argument="layout" type="select" label="Plotting layout" optional="false" help="">
            <expand macro="options_layout"/>
        </param>
    </xml>
    <xml name="param_root">
        <param argument="root" type="text" value="" label="Comma-separated roots" help="If choosing a tree layout, this is the index of the root node or a list of root node indices. If this is a non-empty vector then the supplied node IDs are used as the roots of the trees (or a single tree if the graph is connected). If this is 'None' or an empty list, the root vertices are automatically calculated based on topological sorting.">