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comparison mageck_mle.xml @ 4:b34c9d6373e0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 4478aabdcb10e4787450b1b23944defa7dc38ffe
author iuc
date Mon, 04 Jun 2018 10:58:04 -0400
parents 9cd937788131
children
comparison
equal deleted inserted replaced
3:5dfc0e462f2a 4:b34c9d6373e0
44 44
45 #if $adv.adjust_method: 45 #if $adv.adjust_method:
46 --adjust-method $adv.adjust_method 46 --adjust-method $adv.adjust_method
47 #end if 47 #end if
48 48
49 #if $adv.sgrnaeff_file: 49 #if $adv.sgrnaeff.sgrnaeff_file_select == "yes":
50 --sgrna-efficiency $adv.sgrnaeff_file 50 #set $nindex = int(str($adv.sgrnaeff.sgrnaeff_name_col)) - 1
51 --sgrna-eff-name-column $adv.sgrnaid_col 51 #set $sindex = int(str($adv.sgrnaeff.sgrnaeff_score_col)) - 1
52 --sgrna-eff-score-column $adv.sgrnaeff_col 52 --sgrna-efficiency $adv.sgrnaeff.sgrnaeff_file
53 --sgrna-eff-name-column $nindex
54 --sgrna-eff-score-column $sindex
53 #end if 55 #end if
54 56
55 $adv.remove_outliers 57 $adv.remove_outliers
56 $adv.update_eff 58 $adv.update_eff
57 --threads \${GALAXY_SLOTS:-1} 59 --threads \${GALAXY_SLOTS:-1}
96 <param name="adjust_method" argument="--adjust-method" type="select" optional="true" label="P-Value Adjustment Method" help="Method for sgRNA-level p-value adjustment, including False Discovery Rate (FDR), Holm's method (Holm), or Pounds's method (Pounds). Default: FDR"> 98 <param name="adjust_method" argument="--adjust-method" type="select" optional="true" label="P-Value Adjustment Method" help="Method for sgRNA-level p-value adjustment, including False Discovery Rate (FDR), Holm's method (Holm), or Pounds's method (Pounds). Default: FDR">
97 <option value="fdr">FDR</option> 99 <option value="fdr">FDR</option>
98 <option value="holm">Holm</option> 100 <option value="holm">Holm</option>
99 <option value="pounds">Pounds</option> 101 <option value="pounds">Pounds</option>
100 </param> 102 </param>
101 <param name="sgrnaeff_file" argument="--sgrna-efficiency" type="data" format="tabular" optional="true" label="sgRNA efficiency file" help="An optional file of sgRNA efficiency prediction. The efficiency prediction will be used as an initial guess of the probability an sgRNA is efficient. Must contain at least two columns, one containing sgRNA ID, the other containing sgRNA efficiency prediction" /> 103 <conditional name="sgrnaeff">
102 <param name="sgrnaeff_name_col" argument="--sgrna-eff-score-column" type="data_column" data_ref="sgrnaeff_file" value="1" optional="true" label="sgRNA score column" help="The sgRNA efficiency prediction column in sgRNA efficiency prediction file (specified by the --sgrna-efficiency option). Default is 1 (the second column)." /> 104 <param name="sgrnaeff_file_select" type="select" label="Incorporate sgRNA efficiency" help="Optionally sgRNA efficiency information can be incorporated into the analysis. See the MAGeCK website here for more information: https://sourceforge.net/p/mageck/wiki/Home/#tutorial-3-include-the-sgrna-efficiency-into-mle-calculation">
103 <param name="sgrnaeff_score_col" argument="--sgrna-eff-name-column" type="data_column" data_ref="sgrnaeff_file" value="0" optional="true" label="sgRNA ID column" help="The sgRNA ID column in sgRNA efficiency prediction file (specified by the --sgrna-efficiency option). Default is 0 (the first column)" /> 105 <option value="yes">Yes</option>
106 <option value="no" selected="True">No</option>
107 </param>
108 <when value="yes">
109 <param name="sgrnaeff_file" argument="--sgrna-efficiency" type="data" format="tabular" label="sgRNA efficiency file" help="A file of sgRNA efficiency prediction from the SSC program. The efficiency prediction will be used as an initial guess of the probability an sgRNA is efficient. Must contain at least two columns, one containing sgRNA ID, the other containing sgRNA efficiency prediction." />
110 <param name="sgrnaeff_name_col" argument="--sgrna-eff-name-column" type="data_column" data_ref="sgrnaeff_file" value="1" label="sgRNA ID column" help="The sgRNA ID column in sgRNA efficiency prediction file (specified by the --sgrna-efficiency option). Default is 1 (the first column)" />
111 <param name="sgrnaeff_score_col" argument="--sgrna-eff-score-column" type="data_column" data_ref="sgrnaeff_file" value="2" label="sgRNA score column" help="The sgRNA efficiency prediction column in sgRNA efficiency prediction file (specified by the --sgrna-efficiency option). Default is 2 (the second column)." />
112 </when>
113 <when value="no"/>
114 </conditional>
104 <param name="update_eff" argument="--update-efficiency" type="boolean" truevalue="--update-efficiency" falsevalue="" checked="false" optional="true" 115 <param name="update_eff" argument="--update-efficiency" type="boolean" truevalue="--update-efficiency" falsevalue="" checked="false" optional="true"
105 label="Update efficiency" help="Iteratively update sgRNA efficiency during EM iteration" /> 116 label="Update efficiency" help="Iteratively update sgRNA efficiency during EM iteration" />
106 <param name="out_log" type="boolean" truevalue="True" falsevalue="" checked="false" 117 <param name="out_log" type="boolean" truevalue="True" falsevalue="" checked="false"
107 label="Output Log file" help="This file includes the logging information during the execution. For count command, it will list some basic statistics of the dataset at the end, including the number of reads, the number of reads mapped to the library, the number of zero-count sgRNAs, etc. Default: No" /> 118 label="Output Log file" help="This file includes the logging information during the execution. For count command, it will list some basic statistics of the dataset at the end, including the number of reads, the number of reads mapped to the library, the number of zero-count sgRNAs, etc. Default: No" />
108 </section> 119 </section>
117 <tests> 128 <tests>
118 <test><!-- Ensure MAGeCK's demo1 test works --> 129 <test><!-- Ensure MAGeCK's demo1 test works -->
119 <param name="count_table" value="demo/demo1/sample.txt" ftype="tabular" /> 130 <param name="count_table" value="demo/demo1/sample.txt" ftype="tabular" />
120 <param name="design_matrix" ftype="tabular" value="in.mle.design_matrix.txt" /> 131 <param name="design_matrix" ftype="tabular" value="in.mle.design_matrix.txt" />
121 <param name="out_log" value="True"/> 132 <param name="out_log" value="True"/>
122 <output name="gene_summary" file="out.mle.gene_summary.txt" compare="sim_size"/> 133 <output name="gene_summary">
123 <output name="sgrna_summary" file="out.mle.sgrna_summary.txt"/> 134 <assert_contents>
135 <has_text_matching expression="Gene.*sgRNA.*beta.*z.*p-value.*fdr.*wald-p-value.*wald-fdr.*beta.*p-value.*fdr.*wald-p-value.*wald-fdr" />
136 <has_text_matching expression="A1CF.*10.*0.05018.*0.3479.*0.7278.*0.8665.*0.0927.*0.6435.*0.5198.*0.8170"/>
137 </assert_contents>
138 </output>
139 <output name="sgrna_summary">
140 <assert_contents>
141 <has_text_matching expression="Gene.*sgRNA.*eff" />
142 <has_text_matching expression="ADNP2.*ADNP2_m77891006.*1"/>
143 </assert_contents>
144 </output>
124 <output name="log" file="out.mle.log.txt" compare="sim_size"/> 145 <output name="log" file="out.mle.log.txt" compare="sim_size"/>
146 </test>
147 <test><!-- Ensure sgRNA efficiency file works -->
148 <param name="count_table" value="demo/demo1/sample.txt" ftype="tabular" />
149 <param name="design_matrix" ftype="tabular" value="in.mle.design_matrix.txt" />
150 <param name="sgrnaeff_file_select" value="yes"/>
151 <param name="sgrnaeff_file" value="in.mle.sgrnaeff"/>
152 <param name="sgrnaeff_name_col" value="2"/>
153 <param name="sgrnaeff_score_col" value="4"/>
154 <output name="gene_summary">
155 <assert_contents>
156 <has_text_matching expression="Gene.*sgRNA.*beta.*z.*p-value.*fdr.*wald-p-value.*wald-fdr.*beta.*p-value.*fdr.*wald-p-value.*wald-fdr" />
157 <has_text_matching expression="A1CF.*10.*0.05018.*0.3479.*0.7278.*0.8665.*0.0927.*0.6435.*0.5198.*0.8252"/>
158 </assert_contents>
159 </output>
160 <output name="sgrna_summary">
161 <assert_contents>
162 <has_text_matching expression="Gene.*sgRNA.*eff" />
163 <has_text_matching expression="ADNP2.*ADNP2_m77891006.*0.646"/>
164 </assert_contents>
165 </output>
125 </test> 166 </test>
126 </tests> 167 </tests>
127 168
128 <help><![CDATA[ 169 <help><![CDATA[
129 .. class:: infomark 170 .. class:: infomark