Mercurial > repos > lecorguille > xcms_group
annotate abims_xcms_group.xml @ 11:dc29a74d307b draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit cb8acec98a477af7d69192d5f2dfe977843a7f0f
| author | lecorguille |
|---|---|
| date | Mon, 14 Nov 2016 16:19:18 -0500 |
| parents | 676c748b23ea |
| children | f4dc089f9d19 |
| rev | line source |
|---|---|
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676c748b23ea
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
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1 <tool id="abims_xcms_group" name="xcms.group" version="2.0.6"> |
| 0 | 2 |
| 3 <description>Group peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.</description> | |
| 4 | |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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5 <macros> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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6 <import>macros.xml</import> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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7 </macros> |
| 0 | 8 |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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9 <expand macro="requirements"/> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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10 <expand macro="stdio"/> |
| 0 | 11 |
| 1 | 12 <command><![CDATA[ |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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13 @COMMAND_XCMS_SCRIPT@ |
| 1 | 14 xfunction group |
| 15 image $image | |
| 16 | |
| 17 xsetRdataOutput $xsetRData | |
| 18 rplotspdf $rplotsPdf | |
| 19 | |
| 20 method $methods.method sleep 0.001 | |
| 0 | 21 #if $methods.method == "density": |
| 22 ## minsamp $methods.minsamp | |
| 23 minfrac $methods.minfrac | |
| 24 bw $methods.bw | |
| 25 mzwid $methods.mzwid | |
| 26 #if $methods.density_options.option == "show": | |
| 27 max $methods.density_options.max | |
| 28 #end if | |
| 29 #elif $methods.method == "mzClust": | |
| 30 mzppm $methods.mzppm | |
| 31 mzabs $methods.mzabs | |
| 32 minfrac $methods.minfrac | |
| 33 ## minsamp $methods.minsamp | |
| 34 #else: | |
| 35 mzVsRTbalance $methods.mzVsRTbalance | |
| 36 mzCheck $methods.mzCheck | |
| 37 rtCheck $methods.rtCheck | |
| 38 kNN $methods.kNN | |
| 39 #end if | |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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40 @COMMAND_LOG_EXIT@ |
| 1 | 41 ]]></command> |
| 0 | 42 |
| 43 <inputs> | |
| 44 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" /> | |
| 45 <conditional name="methods"> | |
| 46 <param name="method" type="select" label="Method to use for grouping" help="[method] See the help section below"> | |
| 47 <option value="density" selected="true">density</option> | |
| 48 <option value="mzClust" >mzClust</option> | |
| 49 <option value="nearest" >nearest</option> | |
| 50 </param> | |
| 51 <when value="density"> | |
| 52 <param name="bw" type="integer" value="30" label="Bandwidth" help="[bw] bandwidth (standard deviation or half width at half maximum) of gaussian smoothing kernel to apply to the peak density chromatogram" /> | |
| 53 <param name="minfrac" type="float" value="0.5" label="Minimum fraction of samples necessary" help="[minfrac] in at least one of the sample groups for it to be a valid group" /> | |
| 54 <param name="mzwid" type="float" value="0.25" label="Width of overlapping m/z slices" help="[mzwid] to use for creating peak density chromatograms and grouping peaks across samples " /> | |
| 55 <!-- | |
| 56 <param name="minsamp" type="hidden" value="1" label="minsamp" help="minimum number of samples necessary in at least one of the sample groups for it to be a valid group " /> | |
| 57 --> | |
| 58 <conditional name="density_options"> | |
| 59 <param name="option" type="select" label="Advanced options"> | |
| 60 <option value="show">show</option> | |
| 61 <option value="hide" selected="true">hide</option> | |
| 62 </param> | |
| 63 <when value="show"> | |
| 64 <param name="max" type="integer" value="5" label="Maximum number of groups to identify in a single m/z slice" help="[max]" /> | |
| 65 </when> | |
| 66 <when value="hide"> | |
| 67 </when> | |
| 68 </conditional> | |
| 69 | |
| 70 </when> | |
| 71 <when value="mzClust"> | |
| 72 <param name="mzppm" type="integer" value="20 " label="Relative error used for clustering/grouping in ppm" help="[mzppm]" /> | |
| 73 <param name="mzabs" type="float" value="0" label="Absolute error used for clustering/grouping" help="[mzabs]" /> | |
| 74 <param name="minfrac" type="float" value="0" label="Minimum fraction of each class in one bin" help="[minfrac] minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group" /> | |
| 75 <!-- | |
| 76 <param name="minsamp" type="hidden" value="1" label="minsamp" help="minimum number of samples necessary in at least one of the sample groups for it to be a valid group " /> | |
| 77 --> | |
| 78 </when> | |
| 79 <when value="nearest"> | |
| 80 <param name="mzVsRTbalance" type="integer" value="10 " label="Multiplicator for mz value before calculating the (euclidean) distance between two peaks." help="[mzVsRTbalance]" /> | |
| 81 <param name="mzCheck" type="float" value="0.2" label="Maximum tolerated distance for mz" help="[mzCheck]" /> | |
| 82 <param name="rtCheck" type="integer" value="15" label="Maximum tolerated distance for RT" help="[rtCheck]" /> | |
| 83 <param name="kNN" type="integer" value="10" label="Number of nearest Neighbours to check" help="[kNN]" /> | |
| 84 </when> | |
| 85 </conditional> | |
| 86 <!-- | |
| 87 <param name="sleepy" type="float" value="0.001" label="sleep" help="seconds to pause between plotting successive steps of the peak grouping algorithm. peaks are plotted as points showing relative intensity. identified groups are flanked by dotted vertical lines"> | |
| 88 <validator type="in_range" message="Must be more than 0" min="0.001" max="inf"/> | |
| 89 </param> | |
| 90 --> | |
| 91 | |
| 92 </inputs> | |
| 93 | |
| 94 <outputs> | |
| 95 <data name="xsetRData" format="rdata.xcms.group" label="${image.name[:-6]}.group.RData"/> | |
| 96 <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.group.Rplots.pdf"/> | |
| 1 | 97 <data name="log" format="txt" label="xset.log.txt" hidden="true" /> |
| 0 | 98 </outputs> |
| 99 | |
| 100 <tests> | |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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101 <!--<test> |
| 0 | 102 <param name="image" value="xset.RData"/> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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103 <param name="methods|method" value="density"/> |
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fef3d1b8e7f4
planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
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104 <param name="methods|bw" value="5"/> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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105 <param name="methods|minfrac" value="0.3"/> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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106 <param name="methods|mzwid" value="0.01"/> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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107 <param name="methods|density_options|option" value="show"/> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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108 <param name="methods|density_options|max" value="50"/> |
| 1 | 109 <output name="log"> |
| 110 <assert_contents> | |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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111 <has_text text="object with 4 samples" /> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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112 <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" /> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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113 <has_text text="Mass range: 50.0021-999.9863 m/z" /> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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114 <has_text text="Peaks: 59359 (about 14840 per sample)" /> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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115 <has_text text="Peak Groups: 48998" /> |
| 1 | 116 <has_text text="Sample classes: bio, blank" /> |
| 117 </assert_contents> | |
| 118 </output> | |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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119 </test>--> |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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120 <test> |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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121 <param name="image" value="faahKO.xset.RData"/> |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
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122 <param name="methods|method" value="density"/> |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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123 <param name="methods|bw" value="5"/> |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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124 <param name="methods|minfrac" value="0.3"/> |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
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125 <param name="methods|mzwid" value="0.01"/> |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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126 <param name="methods|density_options|option" value="show"/> |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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127 <param name="methods|density_options|max" value="50"/> |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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128 <output name="log"> |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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129 <assert_contents> |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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130 <has_text text="object with 4 samples" /> |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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131 <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" /> |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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132 <has_text text="Mass range: 200.1-600 m/z" /> |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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133 <has_text text="Peaks: 9251 (about 2313 per sample)" /> |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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134 <has_text text="Peak Groups: 8275" /> |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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135 <has_text text="Sample classes: KO, WT" /> |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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136 </assert_contents> |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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137 </output> |
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138 </test> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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139 <!--<test> |
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140 <param name="image" value="xset.group.retcor.RData"/> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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141 <param name="methods|method" value="density"/> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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142 <param name="methods|bw" value="5"/> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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143 <param name="methods|minfrac" value="0.3"/> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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144 <param name="methods|mzwid" value="0.01"/> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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145 <param name="methods|density_options|option" value="show"/> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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146 <param name="methods|density_options|max" value="50"/> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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147 <output name="log"> |
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148 <assert_contents> |
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149 <has_text text="object with 4 samples" /> |
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150 <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" /> |
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151 <has_text text="Mass range: 50.0021-999.9863 m/z" /> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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152 <has_text text="Peaks: 59359 (about 14840 per sample)" /> |
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planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
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153 <has_text text="Peak Groups: 48958" /> |
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154 <has_text text="Sample classes: bio, blank" /> |
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155 </assert_contents> |
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156 </output> |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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157 </test>--> |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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158 <test> |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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159 <param name="image" value="faahKO.xset.group.retcor.RData"/> |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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160 <param name="methods|method" value="density"/> |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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161 <param name="methods|bw" value="5"/> |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
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162 <param name="methods|minfrac" value="0.3"/> |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
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163 <param name="methods|mzwid" value="0.01"/> |
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75be85d996d9
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
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164 <param name="methods|density_options|option" value="show"/> |
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165 <param name="methods|density_options|max" value="50"/> |
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166 <output name="log"> |
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167 <assert_contents> |
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168 <has_text text="object with 4 samples" /> |
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169 <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" /> |
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170 <has_text text="Mass range: 200.1-600 m/z" /> |
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171 <has_text text="Peaks: 9251 (about 2313 per sample)" /> |
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172 <has_text text="Peak Groups: 8157" /> |
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173 <has_text text="Sample classes: KO, WT" /> |
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174 </assert_contents> |
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175 </output> |
| 0 | 176 </test> |
| 177 </tests> | |
| 178 | |
| 1 | 179 <help><![CDATA[ |
| 0 | 180 |
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181 @HELP_AUTHORS@ |
| 0 | 182 |
| 183 ========== | |
| 184 Xcms.Group | |
| 185 ========== | |
| 186 | |
| 187 ----------- | |
| 188 Description | |
| 189 ----------- | |
| 190 | |
| 191 After peak identification with xcmsSet, this tool groups the peaks which represent the same analyte across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time. Allows rejection of features, which are only partially detected within the replicates of a sample class. | |
| 192 | |
| 193 | |
| 194 | |
| 195 ----------------- | |
| 196 Workflow position | |
| 197 ----------------- | |
| 198 | |
| 199 **Upstream tools** | |
| 200 | |
| 201 ========================= ================= =================== ========== | |
| 202 Name output file format parameter | |
| 203 ========================= ================= =================== ========== | |
| 204 xcms.xcmsSet xset.RData rdata.xcms.raw RData file | |
| 205 ------------------------- ----------------- ------------------- ---------- | |
| 206 xcms.retcor xset.RData rdata.xcms.retcor RData file | |
| 207 ========================= ================= =================== ========== | |
| 208 | |
| 209 | |
| 210 **Downstream tools** | |
| 211 | |
| 212 +---------------------------+--------------------------------------+ | |
| 213 | Name | Output file | Format | | |
| 214 +===========================+=================+====================+ | |
| 215 |xcms.retcor | xset.RData | rdata.xcms.group | | |
| 216 +---------------------------+--------------------------------------+ | |
| 217 |xcms.fillPeaks | xset.RData | rdata.xcms.group | | |
| 218 +---------------------------+--------------------------------------+ | |
| 219 | |
| 220 The output file is an xcmsSet.RData file. You can continue your analysis using it in **xcms.retcor** tool as an next step and then **xcms.fillPeaks**. | |
| 221 | |
| 222 **General schema of the metabolomic workflow** | |
| 223 | |
| 224 .. image:: xcms_group_workflow.png | |
| 225 | |
| 226 | |
| 227 ----------- | |
| 228 Input files | |
| 229 ----------- | |
| 230 | |
| 231 +---------------------------+-----------------------+ | |
| 232 | Parameter : num + label | Format | | |
| 233 +===========================+=======================+ | |
| 234 | 1 : RData file | rdata.xcms.group | | |
| 235 +---------------------------+-----------------------+ | |
| 236 | |
| 237 | |
| 238 ---------- | |
| 239 Parameters | |
| 240 ---------- | |
| 241 | |
| 242 Method to use for grouping | |
| 243 -------------------------- | |
| 244 | |
| 245 **mzClust** | |
| 246 | |
| 247 | Runs high resolution alignment on single spectra samples stored in the RData file generated by the **xcmsSet tool**. | |
| 248 | |
| 249 **density** | |
| 250 | |
| 251 | Groups peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time. | |
| 252 | |
| 253 **nearest** | |
| 254 | |
| 255 | Groups peaks together across samples by creating a master peak list and assigning corresponding peaks from all samples. It is inspired by the alignment algorithm of mzMine. | |
| 256 | |
| 257 | |
| 258 ------------ | |
| 259 Output files | |
| 260 ------------ | |
| 261 | |
| 262 xset.group.Rplots.pdf | |
| 263 | |
| 264 xset.group.RData: rdata.xcms.group format | |
| 265 | |
| 266 | Rdata file that will be necessary in the third and fourth step of the workflow (xcms.retcor and xcms.fillpeaks). | |
| 267 | |
| 268 | |
| 269 ------ | |
| 270 | |
| 271 .. class:: infomark | |
| 272 | |
| 273 The output file is an xset.group.RData file. You can continue your analysis using it in **xcms.retcor** tool. | |
| 274 | |
| 275 | |
| 276 --------------------------------------------------- | |
| 277 | |
| 278 | |
| 279 --------------- | |
| 280 Working example | |
| 281 --------------- | |
| 282 | |
| 283 Input files | |
| 284 ----------- | |
| 285 | |
| 286 | RData file -> **xset.RData** | |
| 287 | |
| 288 Parameters | |
| 289 ---------- | |
| 290 | |
| 291 | Method -> **density** | |
| 292 | bw -> **5** | |
| 293 | minfrac -> **0.3** | |
| 294 | mzwid -> **0.01** | |
| 295 | Advanced options: **show** | |
| 296 | max -> **50** | |
| 297 | |
| 298 | |
| 299 Output files | |
| 300 ------------ | |
| 301 | |
| 302 | **1) xset.RData: RData file** | |
| 303 | |
| 304 | **2) Example of an xset.group.Rplots pdf file** | |
| 305 | |
| 306 .. image:: xcms_group.png | |
| 307 :width: 700 | |
| 308 | |
| 309 | |
| 3 | 310 --------------------------------------------------- |
| 311 | |
| 312 Changelog/News | |
| 313 -------------- | |
| 314 | |
|
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315 **Version 2.0.6 - 06/07/2016** |
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316 |
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317 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0 |
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318 |
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319 **Version 2.0.5 - 04/04/2016** |
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320 |
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321 - TEST: refactoring to pass planemo test using conda dependencies |
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322 |
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323 |
| 3 | 324 **Version 2.0.4 - 10/02/2016** |
| 325 | |
| 326 - BUGFIX: better management of errors. Datasets remained green although the process failed | |
| 327 | |
| 328 - UPDATE: refactoring of internal management of inputs/outputs | |
| 329 | |
| 330 - UPDATE: refactoring to feed the new report tool | |
| 331 | |
| 332 | |
| 333 **Version 2.0.2 - 02/06/2015** | |
| 334 | |
| 335 - IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors. | |
| 336 | |
| 337 - IMPROVEMENT: parameter labels have changed to facilitate their reading. | |
| 338 | |
| 339 | |
| 1 | 340 ]]></help> |
| 0 | 341 |
| 342 | |
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343 <expand macro="citation" /> |
| 0 | 344 |
| 345 | |
| 346 </tool> |