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annotate bandage_image.xml @ 0:067592b6b312 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
author iuc
date Tue, 18 Sep 2018 05:41:44 -0400
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067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
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1 <tool id="bandage_image" name="Bandage Image" version="@TOOL_VERSION@+galaxy0">
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
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2 <description>visualize de novo assembly graphs</description>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
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3 <macros>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
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4 <import>macros.xml</import>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
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5 </macros>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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6 <expand macro="requirements"/>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
iuc
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7 <expand macro="version_command"/>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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8 <command detect_errors="exit_code">
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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9 <![CDATA[
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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10 Bandage
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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11 image
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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12 '$input_file'
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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13 'out.$output_format'
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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14 #if $height:
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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15 --height '$height'
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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16 #end if
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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17 #if $width:
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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18 --width '$width'
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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19 #end if
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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20 ]]></command>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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21 <inputs>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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22 <param name="input_file" type="data" format="tabular" label="Graphical Fragment Assembly" />
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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23 <param argument="--height" type="integer" min="1" value="1000" optional="True" label="Image height" help="If only height or width is set, the other will be determined automatically. If both are set, the image will be exactly that size. Default: 1000."/>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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24 <param argument="--width" type="integer" min="1" optional="True" label="Image width" help="If only height or width is set, the other will be determined automatically. If both are set, the image will be exactly that size. Default: not set."/>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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25 <param name="output_format" type="select" label="Produce jpg, png or svg file?">
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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26 <option selected="True" value="jpg">.jpg</option>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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27 <option value="png">.png</option>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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28 <option value="svg">.svg</option>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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29 </param>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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30 </inputs>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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31 <outputs>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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32 <data name="outfile" format="jpg" from_work_dir="out.*" label="${tool.name} on ${on_string}: Assembly Graph Image">
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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33 <change_format>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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34 <when input="output_format" value="png" format="png"/>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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35 <when input="output_format" value="svg" format="svg"/>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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36 </change_format>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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37 </data>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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38 </outputs>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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39 <tests>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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40 <test>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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41 <param name="input_file" ftype="tabular" value="gfa.tabular"/>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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42 <output name="outfile" ftype="jpg" file="out.jpg" compare="sim_size" delta="70000"/>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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43 </test>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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44 <test>
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45 <param name="input_file" ftype="tabular" value="gfa.tabular"/>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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46 <param name="height" value="100"/>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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47 <param name="width" value="100"/>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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48 <param name="output_format" value="png"/>
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49 <output name="outfile" ftype="png" file="out.png" compare="sim_size" delta="120000"/>
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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50 </test>
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51 <test>
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52 <param name="input_file" ftype="tabular" value="gfa.tabular"/>
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53 <param name="output_format" value="svg"/>
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54 <output name="outfile" ftype="svg" file="out.svg" compare="sim_size" delta="120000"/>
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55 </test>
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56 </tests>
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57 <help><![CDATA[
067592b6b312 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16
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58 @BANDAGE_OVERVIEW@
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59
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60 **Command Documentation**
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61
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62 ``Bandage image`` will generate an image file of the graph visualisation.
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63
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64 .. image:: $PATH_TO_IMAGES/bandage_graph.png
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65 :alt: example bandage plot
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66
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67 ]]></help>
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68 <expand macro="citations"/>
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69 </tool>
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70