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comparison FCSflowAI.xml @ 2:fab7c5deeb65 draft

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planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
author azomics
date Tue, 26 Sep 2023 23:19:04 +0000
parents 34397a84faf1
children dd00eee6cd06
comparison
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1:34397a84faf1 2:fab7c5deeb65
1 <tool id="flowAI" name="flowAI" version="1.0+galaxy0"> 1 <tool id="flowAI" name="flowAI" version="1.0+galaxy1">
2 <description> automatic quality control</description> 2 <description> automatic quality control</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.42.0">bioconductor-flowcore</requirement> 4 <requirement type="package" version="1.42.0">bioconductor-flowcore</requirement>
5 <requirement type="package" version="1.2.9">bioconductor-flowai</requirement> 5 <requirement type="package" version="1.2.9">bioconductor-flowai</requirement>
6 </requirements> 6 </requirements>
7 <stdio> 7 <stdio>
8 <exit_code range="2:" level="fatal" description="See stderr for more details." /> 8 <exit_code range="1:" level="fatal" description="See stderr for more details."/>
9 </stdio> 9 </stdio>
10 <command><![CDATA[ 10 <command><![CDATA[
11 Rscript $__tool_directory__/FCSflowAI.R '${input}' '${remove}' $alphaFR $chremFS $outFS $penFS '${sideFM}' '${full_rep}' $highfcs $lowfcs $qcfcs 11 Rscript $__tool_directory__/FCSflowAI.R '${input}' '${remove}' $alphaFR $chremFS $outFS $penFS '${sideFM}' report.html high.fcs low.fcs qc.fcs &&
12 cp report.html $full_rep
13 #if $highQ_FCS:
14 && cp high.fcs $highfcs
15 #end if
16 #if $lowQ_FCS:
17 && cp low.fcs $lowfcs
18 #end if
19 #if $QC_FCS:
20 && cp qc.fcs $qcfcs
21 #end if
12 ]]> 22 ]]>
13 </command> 23 </command>
14 <inputs> 24 <inputs>
15 <param format="fcs" name="input" type="data" label="FCS file"/> 25 <param format="fcs" name="input" type="data" label="FCS file"/>
16 <param name="remove" type="select" label="Remove low quality cells from:"> 26 <param name="remove" type="select" label="Remove low quality cells from:">
47 <data format="fcs" name="qcfcs" label="All events (low quality event marked up) from ${input.name}"> 57 <data format="fcs" name="qcfcs" label="All events (low quality event marked up) from ${input.name}">
48 <filter>(QC_FCS)</filter> 58 <filter>(QC_FCS)</filter>
49 </data> 59 </data>
50 </outputs> 60 </outputs>
51 <tests> 61 <tests>
52 <test> 62 <test expect_num_outputs="2">
53 <param name="input" value="input.fcs"/> 63 <param name="input" value="input.fcs"/>
54 <param name="remove" value="all"/> 64 <param name="remove" value="all"/>
55 <param name="alphaFR" value="0.01"/> 65 <param name="alphaFR" value="0.01"/>
56 <param name="chremFS" value="TRUE"/> 66 <param name="chremFS" value="TRUE"/>
57 <param name="outFS" value="FALSE"/> 67 <param name="outFS" value="FALSE"/>
58 <param name="penFS" value="200"/> 68 <param name="penFS" value="200"/>
59 <param name="sideFM" value="both"/> 69 <param name="sideFM" value="both"/>
60 <param name="highQ_FCS" value="TRUE"/> 70 <param name="highQ_FCS" value="TRUE"/>
61 <param name="lowQ_FCS" value="FALSE"/> 71 <param name="lowQ_FCS" value="FALSE"/>
62 <param name="QC_FCS" value="FALSE"/> 72 <param name="QC_FCS" value="FALSE"/>
63 <output name="full_rep" file="std/QCreport.html" compare="sim_size"/> 73 <output name="full_rep">
74 <assert_contents>
75 <has_n_lines min="100" max="500"/>
76 <has_text text="data:image/png;base64"/>
77 <has_text text="Dynamic range check"/>
78 <has_text text="total_UNIQUE"/>
79 <has_size value="267939" delta="30000"/>
80 </assert_contents>
81 </output>
64 <output name="highfcs" file="std/hqdata.fcs" compare="sim_size"/> 82 <output name="highfcs" file="std/hqdata.fcs" compare="sim_size"/>
65 </test> 83 </test>
66 <test> 84 <test expect_num_outputs="4">
67 <param name="input" value="input.fcs"/> 85 <param name="input" value="input.fcs"/>
68 <param name="remove" value="all"/> 86 <param name="remove" value="all"/>
69 <param name="alphaFR" value="0.01"/> 87 <param name="alphaFR" value="0.01"/>
70 <param name="chremFS" value="TRUE"/> 88 <param name="chremFS" value="TRUE"/>
71 <param name="outFS" value="FALSE"/> 89 <param name="outFS" value="FALSE"/>
72 <param name="penFS" value="200"/> 90 <param name="penFS" value="200"/>
73 <param name="sideFM" value="both"/> 91 <param name="sideFM" value="both"/>
74 <param name="highQ_FCS" value="TRUE"/> 92 <param name="highQ_FCS" value="TRUE"/>
75 <param name="lowQ_FCS" value="TRUE"/> 93 <param name="lowQ_FCS" value="TRUE"/>
76 <param name="QC_FCS" value="TRUE"/> 94 <param name="QC_FCS" value="TRUE"/>
77 <output name="full_rep" file="std/QCreport.html" compare="sim_size"/> 95 <output name="full_rep">
96 <assert_contents>
97 <has_n_lines min="100" max="500"/>
98 <has_text text="data:image/png;base64"/>
99 <has_text text="Dynamic range check"/>
100 <has_text text="total_UNIQUE"/>
101 <has_size value="267939" delta="30000"/>
102 </assert_contents>
103 </output>
78 <output name="highfcs" file="std/hqdata.fcs" compare="sim_size"/> 104 <output name="highfcs" file="std/hqdata.fcs" compare="sim_size"/>
79 <output name="lowfcs" file="std/lqdata.fcs" compare="sim_size"/> 105 <output name="lowfcs" file="std/lqdata.fcs" compare="sim_size"/>
80 <output name="qcfcs" file="std/alldata.fcs" compare="sim_size"/> 106 <output name="qcfcs" file="std/alldata.fcs" compare="sim_size"/>
81 </test> 107 </test>
82 <test> 108 <test expect_num_outputs="2">
83 <param name="input" value="input.fcs"/> 109 <param name="input" value="input.fcs"/>
84 <param name="remove" value="all"/> 110 <param name="remove" value="all"/>
85 <param name="alphaFR" value="0.01"/> 111 <param name="alphaFR" value="0.01"/>
86 <param name="chremFS" value="TRUE"/> 112 <param name="chremFS" value="TRUE"/>
87 <param name="outFS" value="TRUE"/> 113 <param name="outFS" value="TRUE"/>
88 <param name="penFS" value="200"/> 114 <param name="penFS" value="200"/>
89 <param name="sideFM" value="both"/> 115 <param name="sideFM" value="both"/>
90 <param name="highQ_FCS" value="TRUE"/> 116 <param name="highQ_FCS" value="TRUE"/>
91 <param name="lowQ_FCS" value="FALSE"/> 117 <param name="lowQ_FCS" value="FALSE"/>
92 <param name="QC_FCS" value="FALSE"/> 118 <param name="QC_FCS" value="FALSE"/>
93 <output name="full_rep" file="nooutliers/QCreport_nooutliers.html" compare="sim_size"/> 119 <output name="full_rep">
120 <assert_contents>
121 <has_n_lines min="100" max="500"/>
122 <has_text text="data:image/png;base64"/>
123 <has_text text="Dynamic range check"/>
124 <has_size value="268106" delta="30000"/>
125 </assert_contents>
126 </output>
94 <output name="highfcs" file="nooutliers/hqdata_nooutliers.fcs" compare="sim_size"/> 127 <output name="highfcs" file="nooutliers/hqdata_nooutliers.fcs" compare="sim_size"/>
95 </test> 128 </test>
96 <test> 129 <test expect_num_outputs="2">
97 <param name="input" value="input.fcs"/> 130 <param name="input" value="input.fcs"/>
98 <param name="remove" value="all"/> 131 <param name="remove" value="all"/>
99 <param name="alphaFR" value="0.01"/> 132 <param name="alphaFR" value="0.01"/>
100 <param name="chremFS" value="FALSE"/> 133 <param name="chremFS" value="FALSE"/>
101 <param name="outFS" value="FALSE"/> 134 <param name="outFS" value="FALSE"/>
102 <param name="penFS" value="200"/> 135 <param name="penFS" value="200"/>
103 <param name="sideFM" value="both"/> 136 <param name="sideFM" value="both"/>
104 <param name="highQ_FCS" value="TRUE"/> 137 <param name="highQ_FCS" value="TRUE"/>
105 <param name="lowQ_FCS" value="FALSE"/> 138 <param name="lowQ_FCS" value="FALSE"/>
106 <param name="QC_FCS" value="FALSE"/> 139 <param name="QC_FCS" value="FALSE"/>
107 <output name="full_rep" file="withsfsc/QCreport_sfsc.html" compare="sim_size"/> 140 <output name="full_rep">
141 <assert_contents>
142 <has_n_lines min="100" max="500"/>
143 <has_text text="data:image/png;base64"/>
144 <has_text text="Dynamic range check"/>
145 <has_text text="total_UNIQUE"/>
146 <has_size value="267894" delta="30000"/>
147 </assert_contents>
148 </output>
108 <output name="highfcs" file="withsfsc/hqdata_sfsc.fcs" compare="sim_size"/> 149 <output name="highfcs" file="withsfsc/hqdata_sfsc.fcs" compare="sim_size"/>
109 </test> 150 </test>
110 </tests> 151 </tests>
111 <help><![CDATA[ 152 <help><![CDATA[
112 This tool automatically performs quality control of flow cytometry data. 153 This tool automatically performs quality control of flow cytometry data.