Mercurial > repos > immport-devteam > txt_diagnosis

annotate txtDiagnosis.xml @ 1:b94872d65050 draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
author azomics
date Thu, 16 Jul 2020 07:35:26 -0400
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b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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1 <tool id="txt_diagnosis" name="Check data" version="1.1+galaxy0" profile="18.01">
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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2 <description> in txt-converted FCS files</description>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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3 <requirements>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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4 <requirement type="package" version="0.17.1">pandas</requirement>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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5 </requirements>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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6 <stdio>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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7 <exit_code range="1:" />
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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8 </stdio>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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9 <command><![CDATA[
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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10 python '$__tool_directory__/txtdiagnosis.py' -i '${input}' -o '${output}' -n '${input.name}'
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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11 ]]>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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12 </command>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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13 <inputs>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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14 <param format="flowtext" name="input" type="data" label="Text file to check"/>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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15 </inputs>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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16 <outputs>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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17 <data format="txt" name="output" label="Report on ${input.name}"/>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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18 </outputs>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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19 <tests>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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20 <test>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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21 <param name="input" value="input_error.txt"/>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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22 <output name="output" file="output_error.txt">
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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23 <assert_contents>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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24 <has_text_matching expression="WARNING: line 6 in .* contains non-numeric results"/>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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25 </assert_contents>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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26 </output>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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27 </test>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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28 <test>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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29 <param name="input" value="input_noerror.txt"/>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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30 <output name="output" file="output_noerror.txt">
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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31 <assert_contents>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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32 <has_text text="No errors in the file."/>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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33 </assert_contents>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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34 </output>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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35 </test>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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36 </tests>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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37 <help><![CDATA[
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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38 This tool looks for potential errors in txt-converted FCS files.
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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39 -----
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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40 **Input**
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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41 This diagnosis tools reads in text files, and checks that the data is all numeric.
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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42 **Output**
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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43 The output is a report with the errors and corresponding line numbers.
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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44 -----
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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45 **Example**
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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46 *Input*::
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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47 Marker1 Marker2 Marker3
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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48 34 45 12
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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49 NaN 65 10
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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50 34 45 12
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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51 33 NaN 10
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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52 34 45 12
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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53 33 65 10
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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54 34 45 12
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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55 33 65 NaN
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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56 34 45 12
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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57 33 65 10
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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58 *Output*::
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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59 WARNING: line 2 in example_file.txt contains non-numeric results
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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60 WARNING: line 4 in example_file.txt contains non-numeric results
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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61 WARNING: line 8 in example_file.txt contains non-numeric results
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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62 ]]>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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63 </help>
b94872d65050 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/txt_diagnosis commit 41bbf946c933eb16a0a7d0eac7928e7bf7f465ca"
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64 </tool>